Scientific Question: Given the significant reduction for the risk of breast cancer after obese patients undergo bariatric surgery, what specific genes are responsible for the reduced risk and how do the expression levels of these certain genes change after the surgery?

Hypothesis: If the levels of Estrogen Receptor Alpha decrease after bariatric surgery, then by analyzing the specific gene (ESR1) expression levels of this protein and associated pathways will show a marked change from pre-weight loss surgery levels that are responsible for the preventative phenotype against breast cancer.

The packages Edger and limma are used to filter out lowly expressed counts and to model the voom plot in RNA-seq and also EdgeR is used in Pathway analysis to gain access to cerrtain functions

library(edgeR)
library(limma)

The package msa used to align multiple sequences from a single fasta file with its function msa

library(msa)
seqdata<- read.csv("/Users/heatherotto/Downloads/GSE126803_AI007_Readcounts.csv")
seqdata
dim(seqdata)
[1] 19645    61
countdata<- seqdata[,-(1)]
countdata
rownames(countdata) <- seqdata[,1]
head(countdata)
sampleinfo<- read.delim("/Users/heatherotto/Sampleinfo copy.txt", row.names= NULL)
colnames(sampleinfo) <- colnames(sampleinfo)[2:ncol(sampleinfo)]
sampleinfo
sampleinfo<- sampleinfo[, -(3:4)]
sampleinfo
y<- DGEList(countdata)
y
An object of class "DGEList"
$counts
        AI007_P45_POST AI007_P42_POST AI007_P41_POST AI007_P44_POST AI007_P40_POST AI007_P43_POST
DEPDC1B     0.08969942      0.1377730      0.4689322      0.6425727      0.2710652      0.2390679
CLASP1      8.29223807      6.9066242     10.0749860      9.0827100     12.9326915      8.8306438
TSC2       20.41821708     20.9614251     14.6790392     21.8024361     22.7280129     17.6134194
ERGIC2     24.29453789     31.6844127     36.8340772     33.1361719     33.7938411     34.6500575
SPG20OS     0.51340170      0.4293197      0.0000000      0.0677277      0.8594560      0.3434817
        AI007_P62_POST AI007_P64_POST AI007_P39_POST AI007_P54_POST AI007_P56_POST AI007_P59_POST
DEPDC1B      0.3810158     0.02985079      0.3991934     0.04679104       0.000000      0.1567836
CLASP1       8.5018542     7.41074318      9.2111196     8.82339225       8.252884      8.5378324
TSC2        20.5334382    22.90115266     17.9478907    27.03462975      18.732465     16.9429477
ERGIC2      28.0519829    19.67938260     25.6030502    25.31411789      27.274788     31.6587906
SPG20OS      0.3375794     0.65612606      0.4714289     0.38284594       0.000000      0.3943235
        AI007_P30_POST AI007_P33_POST AI007_P20_POST AI007_P25_POST AI007_P26_POST AI007_P29_POST
DEPDC1B      0.0501999     0.09899953     0.06860305      0.1752291     0.09320857     0.04430422
CLASP1       8.8948742    11.14349889     9.53456943      9.2975701     8.20042424     8.39604851
TSC2        22.7482431    18.68817115    14.17456014     21.7803833    16.24760807    16.16759857
ERGIC2      27.6848779    25.12473641    33.27308743     40.7538765    29.55974952    29.14257278
SPG20OS      0.7444397     0.32698846     0.08126292      0.0000000     0.15388827     0.35194182
        AI007_P17_POST AI007_P69_POST AI007_P2_POST AI007_P8_POST AI007_P19_POST AI007_P15_POST AI007_P58_POST
DEPDC1B      0.3536386      0.1603581    0.02380131    0.09098328     0.13393686     0.06969021     0.03364489
CLASP1       9.6874216     11.2414363    4.81093742    8.95276389     9.40307322     8.58215847     6.31334240
TSC2        16.2564699     16.5288894   11.98917274   18.41631154    21.51137553    15.50351101    15.23328212
ERGIC2      34.8356066     36.1047479   17.25532438   31.16564676    38.77159560    34.22509806    36.16802991
SPG20OS      1.1519228      0.1827098    0.37986174    0.05784366     0.05784366     0.42124056     0.28019428
        AI007_P1_POST AI007_P37_POST AI007_P53_POST AI007_P55_POST AI007_P5_POST AI007_P44_PRE AI007_P45_PRE
DEPDC1B     0.4911890      0.3610493      0.1136028     0.09291356    0.01116544       0.00000    0.05779537
CLASP1      8.8250530     11.4324839      8.2329628     7.89373506   11.08134880      12.52725   10.05180875
TSC2       14.4110359     19.3913762     19.0121881    19.86529843   19.42022476      23.86788   25.82734610
ERGIC2     40.6769330     16.2188413     32.0814595    36.98349010   28.48121922      24.21277   27.16994391
SPG20OS     0.4795911      0.1835943      0.3755042     0.05213495    1.56143639       0.00000    0.29807249
        AI007_P41_PRE AI007_P40_PRE AI007_P42_PRE AI007_P43_PRE AI007_P64_PRE AI007_P39_PRE AI007_P54_PRE
DEPDC1B    0.19430432     0.2393998     0.1357762    0.06355554    0.02536228     0.1194512     0.1759087
CLASP1    12.04448929     8.6591094     8.3761595    9.35402683    5.99278228     9.2258454     8.6915694
TSC2      14.85757132    15.4644994    14.3929859   22.85739826   32.78989079    16.0272630    23.8790380
ERGIC2    31.08928686    36.3008713    27.5867316   52.14664520   15.80894345    33.7884990    25.5698107
SPG20OS    0.09558827     0.1267672     0.0000000    0.39923433    0.30728566     0.0000000     1.2991460
        AI007_P56_PRE AI007_P59_PRE AI007_P62_PRE AI007_P33_PRE AI007_P20_PRE AI007_P25_PRE AI007_P26_PRE
DEPDC1B    0.03254789    0.07536732     0.1879747    0.07500112    0.23588178    0.22121742    0.24536749
CLASP1     8.59145698    8.92918670    10.2306575    7.69298607    4.63658607   10.72337215    8.79752802
TSC2      19.74323945   20.30813567    19.6965824   17.38359714   28.39474488   20.30840905   15.84455339
ERGIC2    24.17770466   31.09084848    35.7840620   23.88359358    9.94057162   21.77228556   34.61117909
SPG20OS    0.06013589    0.09353621     0.1749615    0.09183099    0.08263845    0.07534792    0.07605192
        AI007_P29_PRE AI007_P30_PRE AI007_P69_PRE AI007_P2_PRE AI007_P8_PRE AI007_P19_PRE AI007_P15_PRE
DEPDC1B    0.03151935    0.02822746     0.2077901   0.09047029 9.650265e-04     0.3415222     0.2326068
CLASP1    11.58481344   10.31491832     9.7284928   9.38149203 7.210589e+00    11.0368002     6.2912171
TSC2      18.91443947   16.63015918    19.3889038  17.18876511 1.596532e+01    14.3247503    27.8789860
ERGIC2    25.76242226   33.89741809    29.5176014  31.56035801 2.612456e+01    30.6970516    18.1402925
SPG20OS    0.80623522    0.34338226     0.4916952   0.80873645 5.784366e-02     0.2776951     0.1834748
        AI007_P17_PRE AI007_P1_PRE AI007_P37_PRE AI007_P53_PRE AI007_P55_PRE AI007_P58_PRE AI007_P5_PRE
DEPDC1B    0.36919153    0.1681029    0.05386508    0.01116544    0.16008039     0.2963357   0.01116544
CLASP1    11.24710885    8.8419275   12.24037933   11.55106685    8.44684402     6.7596874   8.82584809
TSC2      22.02743093   22.4983255   14.26515557   28.16410194   18.75746435    23.1045227  17.81352521
ERGIC2    26.32010071   29.1152262   35.10153190   31.64211155   35.30127013    23.5141753  28.86583911
SPG20OS    0.05784366    0.1847546    0.19649589    0.47239067    0.05213495     0.4902792   0.05213495
19640 more rows ...

$samples
55 more rows ...
group<- paste(sampleinfo$Surgery.Status, sep= ".")
group
 [1] "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s"
[10] "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s"
[19] "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s" "  post.s"
[28] "  post.s" "  post.s" "  post.s" "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s" 
[37] "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s" 
[46] "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s" 
[55] "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s"  "  pre.s" 
group<- factor(group)
group
 [1]   post.s   post.s   post.s   post.s   post.s   post.s   post.s   post.s   post.s   post.s   post.s   post.s
[13]   post.s   post.s   post.s   post.s   post.s   post.s   post.s   post.s   post.s   post.s   post.s   post.s
[25]   post.s   post.s   post.s   post.s   post.s   post.s   pre.s    pre.s    pre.s    pre.s    pre.s    pre.s 
[37]   pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s 
[49]   pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s    pre.s 
Levels:   post.s   pre.s
y$samples$group<- group
y$samples
CPM<- cpm(countdata)
head(CPM)
        AI007_P45_POST AI007_P42_POST AI007_P41_POST AI007_P44_POST AI007_P40_POST AI007_P43_POST
DEPDC1B      0.1376810       0.184955      0.7766311      1.0253981      0.4459015      0.3555442
CLASP1      12.7278790       9.271876     16.6858846     14.4939145     21.2742457     13.1330206
TSC2        31.3402237      28.139903     24.3109770     34.7916695     37.3875254     26.1948512
ERGIC2      37.2900458      42.535099     61.0034754     52.8777032     55.5907855     51.5319075
SPG20OS      0.7880279       0.576345      0.0000000      0.1080778      1.4138030      0.5108293
HLX          9.9572347       9.841279     19.1784913      6.9123182     14.0398512      5.4306752
        AI007_P62_POST AI007_P64_POST AI007_P39_POST AI007_P54_POST AI007_P56_POST AI007_P59_POST
DEPDC1B      0.6073717     0.04975775      0.6134787     0.07298751        0.00000      0.2487687
CLASP1      13.5526799    12.35283775     14.1556083    13.76326557       13.13182     13.5469914
TSC2        32.7320500    38.17352944     27.5822399    42.17026495       29.80672     26.8834005
ERGIC2      44.7172508    32.80321746     39.3466555    39.48650557       43.39909     50.2330503
SPG20OS      0.5381304     1.09368501      0.7244898     0.59718645        0.00000      0.6256736
HLX          6.2637551    11.17865870      7.8712893     9.16736771       14.37628     16.5960244
        AI007_P30_POST AI007_P33_POST AI007_P20_POST AI007_P25_POST AI007_P26_POST AI007_P29_POST
DEPDC1B     0.07689474      0.1507720     0.09786017      0.2619113      0.1575402     0.06453105
CLASP1     13.62490813     16.9710611    13.60077467     13.8968860     13.8602742    12.22921493
TSC2       34.84509333     28.4612667    20.21958098     32.5546891     27.4615431    23.54882032
ERGIC2     42.40688611     38.2638739    47.46305203     60.9139775     49.9615901    42.44744246
SPG20OS     1.14031090      0.4979891     0.11591909      0.0000000      0.2601004     0.51261878
HLX        12.51026812      9.9915607     9.51009805      6.5911767     16.6818535     9.58529041
        AI007_P17_POST AI007_P69_POST AI007_P2_POST AI007_P8_POST AI007_P19_POST AI007_P15_POST AI007_P58_POST
DEPDC1B      0.5359515      0.2541925    0.03687605    0.12318349     0.19023079      0.1071199     0.04977093
CLASP1      14.6816209     17.8194199    7.45372347   12.12126812    13.35520409     13.1915221     9.33933450
TSC2        24.6372396     26.2008531   18.57516955   24.93409328    30.55265058     23.8302414    22.53461135
ERGIC2      52.7945608     57.2316248   26.73416947   42.19559069    55.06737638     52.6069447    53.50340727
SPG20OS      1.7457787      0.2896233    0.58853070    0.07831531     0.08215546      0.6474833     0.41449171
HLX          7.6478274     16.6786706    8.02720308   11.32261966    13.50681928     10.7993960     7.80634047
        AI007_P1_POST AI007_P37_POST AI007_P53_POST AI007_P55_POST AI007_P5_POST AI007_P44_PRE AI007_P45_PRE
DEPDC1B     0.7653514      0.5558158      0.1740532     0.15371699    0.01438479       0.00000    0.08903184
CLASP1     13.7508529     17.5996884     12.6138910    13.05946325   14.27644892      19.81262   15.48447534
TSC2       22.4547134     29.8519711     29.1289630    32.86532077   25.01968414      37.74851   39.78616320
ERGIC2     63.3812084     24.9680258     49.1526615    61.18580445   36.69324724      38.29398   41.85439024
SPG20OS     0.7472800      0.2826335      0.5753177     0.08625252    2.01164743       0.00000    0.45917070
HLX         5.8293813     14.4568159     11.9185654     8.91259009   10.87532853      12.23494   11.41288168
        AI007_P41_PRE AI007_P40_PRE AI007_P42_PRE AI007_P43_PRE AI007_P64_PRE AI007_P39_PRE AI007_P54_PRE
DEPDC1B     0.3333328     0.3947641     0.2043082    0.09667073    0.03777452     0.1960563     0.3068482
CLASP1     20.6625532    14.2786513    12.6039606   14.22788015    8.92563489    15.1424610    15.1612252
TSC2       25.4884495    25.5005665    21.6577332   34.76709325   48.83718109    26.3056873    41.6536366
ERGIC2     53.3342700    59.8592141    41.5109191   79.31730708   23.54580072    55.4573597    44.6029527
SPG20OS     0.1639835     0.2090360     0.0000000    0.60725272    0.45767049     0.0000000     2.2661783
HLX        17.4088069    12.6010172    10.0983550    6.03572098   15.45410992    10.6818107     8.5080819
        AI007_P56_PRE AI007_P59_PRE AI007_P62_PRE AI007_P33_PRE AI007_P20_PRE AI007_P25_PRE AI007_P26_PRE
DEPDC1B    0.05408842     0.1239154     0.3031964     0.1099199     0.3931737     0.3679884     0.3869206
CLASP1    14.27737042    14.6809426    16.5016818    11.2746586     7.7283789    17.8379990    13.8728423
TSC2      32.80951573    33.3896675    31.7698775    25.4769891    47.3290790    33.7824125    24.9853128
ERGIC2    40.17875502    51.1180893    57.7184021    35.0032303    16.5691962    36.2175259    54.5784482
SPG20OS    0.09993444     0.1537878     0.2822066     0.1345853     0.1377439     0.1253389     0.1199264
HLX       10.53306579    18.4490750     8.6836860    11.6405492     5.8029265     7.0288823    15.7095021
        AI007_P29_PRE AI007_P30_PRE AI007_P69_PRE AI007_P2_PRE AI007_P8_PRE AI007_P19_PRE AI007_P15_PRE
DEPDC1B    0.05036387    0.04245563     0.3515309    0.1448049  0.001221554     0.5517809     0.3788969
CLASP1    18.51104419   15.51419290    16.4582718   15.0158282  9.127337396    17.8316263    10.2478628
TSC2      30.22284533   25.01265542    32.8013656   27.5119932 20.209282551    23.1438088    45.4125204
ERGIC2    41.16504244   50.98354316    49.9366880   50.5148769 33.069097494    49.5957469    29.5490089
SPG20OS    1.28826035    0.51646543     0.8318301    1.2944474  0.073219893     0.4486587     0.2988650
HLX       10.73029358   17.32316123    14.3502361    3.7544269  9.520771392    13.0328029     8.2901708
        AI007_P17_PRE AI007_P1_PRE AI007_P37_PRE AI007_P53_PRE AI007_P55_PRE AI007_P58_PRE AI007_P5_PRE
DEPDC1B    0.58057106    0.2821525    0.08606747    0.01869908    0.25238204     0.4132298   0.01415905
CLASP1    17.68660801   14.8407452   19.55809704   19.34489523   13.31725704     9.4261484  11.19217670
TSC2      34.63917185   37.7623452   22.79335381   47.16721045   29.57293557    32.2184511  22.58957098
ERGIC2    41.38959712   48.8684912   56.08642907   52.99193057   55.65582680    32.7896973  36.60515893
SPG20OS    0.09096187    0.3101016    0.31396785    0.79112588    0.08219574     0.6836773   0.06611304
HLX        6.84981814   13.4309882   11.45157177   13.50679998    6.81095190     7.2381350  15.63307167
plot(CPM[,1], countdata[,1], ylim= c(0,50), xlim= c(0,30))
abline(v= 18)

thresh<- CPM > 18
head(thresh)
        AI007_P45_POST AI007_P42_POST AI007_P41_POST AI007_P44_POST AI007_P40_POST AI007_P43_POST
DEPDC1B          FALSE          FALSE          FALSE          FALSE          FALSE          FALSE
CLASP1           FALSE          FALSE          FALSE          FALSE           TRUE          FALSE
TSC2              TRUE           TRUE           TRUE           TRUE           TRUE           TRUE
ERGIC2            TRUE           TRUE           TRUE           TRUE           TRUE           TRUE
SPG20OS          FALSE          FALSE          FALSE          FALSE          FALSE          FALSE
HLX              FALSE          FALSE           TRUE          FALSE          FALSE          FALSE
        AI007_P62_POST AI007_P64_POST AI007_P39_POST AI007_P54_POST AI007_P56_POST AI007_P59_POST
DEPDC1B          FALSE          FALSE          FALSE          FALSE          FALSE          FALSE
CLASP1           FALSE          FALSE          FALSE          FALSE          FALSE          FALSE
TSC2              TRUE           TRUE           TRUE           TRUE           TRUE           TRUE
ERGIC2            TRUE           TRUE           TRUE           TRUE           TRUE           TRUE
SPG20OS          FALSE          FALSE          FALSE          FALSE          FALSE          FALSE
HLX              FALSE          FALSE          FALSE          FALSE          FALSE          FALSE
        AI007_P30_POST AI007_P33_POST AI007_P20_POST AI007_P25_POST AI007_P26_POST AI007_P29_POST
DEPDC1B          FALSE          FALSE          FALSE          FALSE          FALSE          FALSE
CLASP1           FALSE          FALSE          FALSE          FALSE          FALSE          FALSE
TSC2              TRUE           TRUE           TRUE           TRUE           TRUE           TRUE
ERGIC2            TRUE           TRUE           TRUE           TRUE           TRUE           TRUE
SPG20OS          FALSE          FALSE          FALSE          FALSE          FALSE          FALSE
HLX              FALSE          FALSE          FALSE          FALSE          FALSE          FALSE
        AI007_P17_POST AI007_P69_POST AI007_P2_POST AI007_P8_POST AI007_P19_POST AI007_P15_POST AI007_P58_POST
DEPDC1B          FALSE          FALSE         FALSE         FALSE          FALSE          FALSE          FALSE
CLASP1           FALSE          FALSE         FALSE         FALSE          FALSE          FALSE          FALSE
TSC2              TRUE           TRUE          TRUE          TRUE           TRUE           TRUE           TRUE
ERGIC2            TRUE           TRUE          TRUE          TRUE           TRUE           TRUE           TRUE
SPG20OS          FALSE          FALSE         FALSE         FALSE          FALSE          FALSE          FALSE
HLX              FALSE          FALSE         FALSE         FALSE          FALSE          FALSE          FALSE
        AI007_P1_POST AI007_P37_POST AI007_P53_POST AI007_P55_POST AI007_P5_POST AI007_P44_PRE AI007_P45_PRE
DEPDC1B         FALSE          FALSE          FALSE          FALSE         FALSE         FALSE         FALSE
CLASP1          FALSE          FALSE          FALSE          FALSE         FALSE          TRUE         FALSE
TSC2             TRUE           TRUE           TRUE           TRUE          TRUE          TRUE          TRUE
ERGIC2           TRUE           TRUE           TRUE           TRUE          TRUE          TRUE          TRUE
SPG20OS         FALSE          FALSE          FALSE          FALSE         FALSE         FALSE         FALSE
HLX             FALSE          FALSE          FALSE          FALSE         FALSE         FALSE         FALSE
        AI007_P41_PRE AI007_P40_PRE AI007_P42_PRE AI007_P43_PRE AI007_P64_PRE AI007_P39_PRE AI007_P54_PRE
DEPDC1B         FALSE         FALSE         FALSE         FALSE         FALSE         FALSE         FALSE
CLASP1           TRUE         FALSE         FALSE         FALSE         FALSE         FALSE         FALSE
TSC2             TRUE          TRUE          TRUE          TRUE          TRUE          TRUE          TRUE
ERGIC2           TRUE          TRUE          TRUE          TRUE          TRUE          TRUE          TRUE
SPG20OS         FALSE         FALSE         FALSE         FALSE         FALSE         FALSE         FALSE
HLX             FALSE         FALSE         FALSE         FALSE         FALSE         FALSE         FALSE
        AI007_P56_PRE AI007_P59_PRE AI007_P62_PRE AI007_P33_PRE AI007_P20_PRE AI007_P25_PRE AI007_P26_PRE
DEPDC1B         FALSE         FALSE         FALSE         FALSE         FALSE         FALSE         FALSE
CLASP1          FALSE         FALSE         FALSE         FALSE         FALSE         FALSE         FALSE
TSC2             TRUE          TRUE          TRUE          TRUE          TRUE          TRUE          TRUE
ERGIC2           TRUE          TRUE          TRUE          TRUE         FALSE          TRUE          TRUE
SPG20OS         FALSE         FALSE         FALSE         FALSE         FALSE         FALSE         FALSE
HLX             FALSE          TRUE         FALSE         FALSE         FALSE         FALSE         FALSE
        AI007_P29_PRE AI007_P30_PRE AI007_P69_PRE AI007_P2_PRE AI007_P8_PRE AI007_P19_PRE AI007_P15_PRE
DEPDC1B         FALSE         FALSE         FALSE        FALSE        FALSE         FALSE         FALSE
CLASP1           TRUE         FALSE         FALSE        FALSE        FALSE         FALSE         FALSE
TSC2             TRUE          TRUE          TRUE         TRUE         TRUE          TRUE          TRUE
ERGIC2           TRUE          TRUE          TRUE         TRUE         TRUE          TRUE          TRUE
SPG20OS         FALSE         FALSE         FALSE        FALSE        FALSE         FALSE         FALSE
HLX             FALSE         FALSE         FALSE        FALSE        FALSE         FALSE         FALSE
        AI007_P17_PRE AI007_P1_PRE AI007_P37_PRE AI007_P53_PRE AI007_P55_PRE AI007_P58_PRE AI007_P5_PRE
DEPDC1B         FALSE        FALSE         FALSE         FALSE         FALSE         FALSE        FALSE
CLASP1          FALSE        FALSE          TRUE          TRUE         FALSE         FALSE        FALSE
TSC2             TRUE         TRUE          TRUE          TRUE          TRUE          TRUE         TRUE
ERGIC2           TRUE         TRUE          TRUE          TRUE          TRUE          TRUE         TRUE
SPG20OS         FALSE        FALSE         FALSE         FALSE         FALSE         FALSE        FALSE
HLX             FALSE        FALSE         FALSE         FALSE         FALSE         FALSE        FALSE
table(rowSums(thresh))

    0     1     2     3     4     5     6     7     8     9    10    11    12    13    14    15    16    17 
11088   414   301   212   177   120   136   126    96    85    88    83    79    66    61    51    51    75 
   18    19    20    21    22    23    24    25    26    27    28    29    30    31    32    33    34    35 
   72    59    76    58    67    56    47    51    41    57    54    56    59    58    43    55    56    48 
   36    37    38    39    40    41    42    43    44    45    46    47    48    49    50    51    52    53 
   62    48    64    43    55    56    63    50    64    61    69    68    73    72    74    99    99   122 
   54    55    56    57    58    59    60 
  116   146   184   181   251   405  2798 
keep<- rowSums(thresh) >= 2
summary(keep)
   Mode   FALSE    TRUE 
logical   11502    8143 
y <- y[keep,keep.lib.size=FALSE]
y<- calcNormFactors(y)
y
An object of class "DGEList"
$counts
       AI007_P45_POST AI007_P42_POST AI007_P41_POST AI007_P44_POST AI007_P40_POST AI007_P43_POST AI007_P62_POST
CLASP1       8.292238       6.906624      10.074986       9.082710      12.932691       8.830644       8.501854
TSC2        20.418217      20.961425      14.679039      21.802436      22.728013      17.613419      20.533438
ERGIC2      24.294538      31.684413      36.834077      33.136172      33.793841      34.650058      28.051983
HLX          6.487158       7.330773      11.580029       4.331651       8.534877       3.651586       3.929373
CP          11.511853      25.831897       6.207498       5.939641       2.835163      30.697666       0.000000
       AI007_P64_POST AI007_P39_POST AI007_P54_POST AI007_P56_POST AI007_P59_POST AI007_P30_POST AI007_P33_POST
CLASP1       7.410743       9.211120       8.823392      8.2528837       8.537832       8.894874      11.143499
TSC2        22.901153      17.947891      27.034630     18.7324655      16.942948      22.748243      18.688171
ERGIC2      19.679383      25.603050      25.314118     27.2747882      31.658791      27.684878      25.124736
HLX          6.706327       5.121884       5.877041      9.0349844      10.459450       8.167194       6.560635
CP           4.533726      11.995819      15.971785      0.2165844       0.000000       9.457096       8.434184
       AI007_P20_POST AI007_P25_POST AI007_P26_POST AI007_P29_POST AI007_P17_POST AI007_P69_POST AI007_P2_POST
CLASP1       9.534569       9.297570       8.200424     8.39604851       9.687422      11.241436      4.810937
TSC2        14.174560      21.780383      16.247608    16.16759857      16.256470      16.528889     11.989173
ERGIC2      33.273087      40.753877      29.559750    29.14257278      34.835607      36.104748     17.255324
HLX          6.666877       4.409760       9.869810     6.58084462       5.046291      10.521791      5.181085
CP           1.926218       7.186049       5.628690     0.05368532      10.312428       9.599091     10.747973
       AI007_P8_POST AI007_P19_POST AI007_P15_POST AI007_P58_POST AI007_P1_POST AI007_P37_POST AI007_P53_POST
CLASP1      8.952764       9.403073       8.582158       6.313342      8.825053      11.432484       8.232963
TSC2       18.416312      21.511376      15.503511      15.233282     14.411036      19.391376      19.012188
ERGIC2     31.165647      38.771596      34.225098      36.168030     40.676933      16.218841      32.081459
HLX         8.362882       9.509822       7.025886       5.277046      3.741193       9.390923       7.779131
CP          9.636731       8.296421       7.785506       9.009380      1.378040       5.245250      12.632921
       AI007_P55_POST AI007_P5_POST AI007_P44_PRE AI007_P45_PRE AI007_P41_PRE AI007_P40_PRE AI007_P42_PRE
CLASP1       7.893735     11.081349     12.527255     10.051809      12.04449      8.659109      8.376159
TSC2        19.865298     19.420225     23.867881     25.827346      14.85757     15.464499     14.392986
ERGIC2      36.983490     28.481219     24.212771     27.169944      31.08929     36.300871     27.586732
HLX          5.387176      8.441407      7.735992      7.408718      10.14784      7.641729      6.711020
CP          22.889810     10.502402     10.242538     20.321663      16.69494     18.587691      4.962621
       AI007_P43_PRE AI007_P64_PRE AI007_P39_PRE AI007_P54_PRE AI007_P56_PRE AI007_P59_PRE AI007_P62_PRE
CLASP1      9.354027      5.992782      9.225845      8.691569     8.5914570      8.929187     10.230658
TSC2       22.857398     32.789891     16.027263     23.879038    19.7432395     20.308136     19.696582
ERGIC2     52.146645     15.808943     33.788499     25.569811    24.1777047     31.090848     35.784062
HLX         3.968145     10.376082      6.508106      4.877481     6.3383087     11.221026      5.383683
CP          7.048288      0.000000      4.897516     20.190741     0.2995237      1.952987      6.241647
       AI007_P33_PRE AI007_P20_PRE AI007_P25_PRE AI007_P26_PRE AI007_P29_PRE AI007_P30_PRE AI007_P69_PRE
CLASP1      7.692986      4.636586    10.7233721      8.797528     11.584813      10.31492      9.728493
TSC2       17.383597     28.394745    20.3084091     15.844553     18.914439      16.63016     19.388904
ERGIC2     23.883594      9.940572    21.7722856     34.611179     25.762422      33.89742     29.517601
HLX         7.942643      3.481425     4.2254358      9.962254      6.715367      11.51765      8.482432
CP         16.296264      0.000000     0.3450054     15.404036      5.236207       5.01858     12.467803
       AI007_P2_PRE AI007_P8_PRE AI007_P19_PRE AI007_P15_PRE AI007_P17_PRE AI007_P1_PRE AI007_P37_PRE
CLASP1     9.381492     7.210589     11.036800      6.291217     11.247109     8.841927     12.240379
TSC2      17.188765    15.965317     14.324750     27.878986     22.027431    22.498326     14.265156
ERGIC2    31.560358    26.124560     30.697052     18.140293     26.320101    29.115226     35.101532
HLX        2.345667     7.521402      8.066591      5.089380      4.355875     8.002012      7.166934
CP        78.443385    12.113838      7.752517      6.637065      7.552611     3.457671      4.392075
       AI007_P53_PRE AI007_P55_PRE AI007_P58_PRE AI007_P5_PRE
CLASP1     11.551067      8.446844      6.759687     8.825848
TSC2       28.164102     18.757464     23.104523    17.813525
ERGIC2     31.642112     35.301270     23.514175    28.865839
HLX         8.065071      4.320037      5.190617    12.327818
CP          3.008328      6.152549      2.868452    26.953178
8138 more rows ...

$samples
55 more rows ...
design<- model.matrix(~0+group)
colnames(design) <- levels(group)
design
     post.s   pre.s
1         1       0
2         1       0
3         1       0
4         1       0
5         1       0
6         1       0
7         1       0
8         1       0
9         1       0
10        1       0
11        1       0
12        1       0
13        1       0
14        1       0
15        1       0
16        1       0
17        1       0
18        1       0
19        1       0
20        1       0
21        1       0
22        1       0
23        1       0
24        1       0
25        1       0
26        1       0
27        1       0
28        1       0
29        1       0
30        1       0
31        0       1
32        0       1
33        0       1
34        0       1
35        0       1
36        0       1
37        0       1
38        0       1
39        0       1
40        0       1
41        0       1
42        0       1
43        0       1
44        0       1
45        0       1
46        0       1
47        0       1
48        0       1
49        0       1
50        0       1
51        0       1
52        0       1
53        0       1
54        0       1
55        0       1
56        0       1
57        0       1
58        0       1
59        0       1
60        0       1
attr(,"assign")
[1] 1 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"
par(mfrow= c(1,1))
v<- voom(y,design, plot= TRUE)

v
An object of class "EList"
$targets
55 more rows ...

$E
       AI007_P45_POST AI007_P42_POST AI007_P41_POST AI007_P44_POST AI007_P40_POST AI007_P43_POST AI007_P62_POST
CLASP1       3.777680       3.499812       3.995957       3.863328       4.350648       3.779075      3.9406886
TSC2         5.028137       5.034670       4.517381       5.082024       5.140765       4.736085      5.1650792
ERGIC2       5.273400       5.619286       5.815794       5.674836       5.702849       5.692554      5.6059855
HLX          3.446155       3.580151       4.187925       2.875411       3.778476       2.610761      2.9175689
CP           4.227836       5.329735       3.339148       3.289875       2.340729       5.520465     -0.2295336
       AI007_P64_POST AI007_P39_POST AI007_P54_POST AI007_P56_POST AI007_P59_POST AI007_P30_POST AI007_P33_POST
CLASP1       3.723906       3.920196       3.865721      3.9113302      3.8097907       3.757951       4.247978
TSC2         5.288600       4.845943       5.428042      5.0470436      4.7583859       5.065127       4.968671
ERGIC2       5.074903       5.346705       5.334955      5.5772758      5.6409552       5.342927       5.385991
HLX          3.589357       3.131612       3.317754      4.0348023      4.0879174       3.641642       3.526324
CP           3.071719       4.283932       4.686791      0.3007802     -0.3661861       3.841803       3.865861
       AI007_P20_POST AI007_P25_POST AI007_P26_POST AI007_P29_POST AI007_P17_POST AI007_P69_POST AI007_P2_POST
CLASP1       4.021887       3.866923       3.811409      3.8679597       3.910493       4.208907      3.591905
TSC2         4.570225       5.052201       4.756206      4.7737694       4.628422       4.745282      4.825545
ERGIC2       5.772782       5.940957       5.600084      5.6043939       5.704826       5.849329      5.333119
HLX          3.536324       2.870151       4.064640      3.5387165       3.033299       4.117657      3.689105
CP           1.973689       3.516741       3.305902     -0.1380667       3.996394       3.991523      4.674532
       AI007_P8_POST AI007_P19_POST AI007_P15_POST AI007_P58_POST AI007_P1_POST AI007_P37_POST AI007_P53_POST
CLASP1      3.948276       3.814100       3.924495       3.546996      3.843889       4.161987       3.793757
TSC2        4.949099       4.966402       4.741777       4.754381      4.521086       4.899236       4.953590
ERGIC2      5.692387       5.801638       5.859367       5.975084      5.986542       4.648568       5.693266
HLX         3.855316       3.829569       3.653321       3.308965      2.707247       3.891270       3.716766
CP          4.049061       3.643141       3.792050       4.027984      1.532005       3.107535       4.382402
       AI007_P55_POST AI007_P5_POST AI007_P44_PRE AI007_P45_PRE AI007_P41_PRE AI007_P40_PRE AI007_P42_PRE
CLASP1       3.726037      4.138434      4.336063      3.944319      4.230665      3.725594      3.822706
TSC2         5.004765      4.920865      5.239511      5.263390      4.522562      4.527182      4.569332
ERGIC2       5.884908      5.461749      5.259787      5.335148      5.563047      5.732055      5.484587
HLX          3.214300      3.765205      3.674545      3.528344      3.994172      3.555722      3.522974
CP           5.204532      4.064449      4.057865      4.924914      4.685596      4.784957      3.122364
       AI007_P43_PRE AI007_P64_PRE AI007_P39_PRE AI007_P54_PRE AI007_P56_PRE AI007_P59_PRE AI007_P62_PRE
CLASP1      4.154996     3.4985153      3.988573      3.855114     3.9566894      3.842557      4.031387
TSC2        5.400090     5.8566907      4.753525      5.262372     5.1115462      4.984499      4.943759
ERGIC2      6.572552     4.8272698      5.806402      5.359111     5.3973142      5.586858      5.788984
HLX         3.013959     4.2427654      3.515774      3.081733     3.5458175      4.156450      3.164440
CP          3.770432    -0.2003216      3.139045      5.025716     0.4493907      1.899963      3.360821
       AI007_P33_PRE AI007_P20_PRE AI007_P25_PRE AI007_P26_PRE AI007_P29_PRE AI007_P30_PRE AI007_P69_PRE
CLASP1      3.800341     3.4019002     4.2382349      3.811574      4.243918      4.223056      3.996602
TSC2        4.926516     5.8938256     5.1288954      4.625465      4.927853      4.886572      4.955973
ERGIC2      5.373790     4.4252192     5.2269783      5.728585      5.363722      5.892334      5.549817
HLX         3.843646     3.0343751     2.9902480      3.981849      3.499867      4.375188      3.809187
CP          4.836020     0.0410904     0.5068331      4.586048      3.168891      3.252403      4.338943
       AI007_P2_PRE AI007_P8_PRE AI007_P19_PRE AI007_P15_PRE AI007_P17_PRE AI007_P1_PRE AI007_P37_PRE
CLASP1     3.883110     3.631263      4.306334      3.603371      4.172570     3.786341      4.339511
TSC2       4.723142     4.725780      4.668099      5.666452      5.111947     5.086078      4.552299
ERGIC2     5.581099     5.419107      5.741500      5.060053      5.363579     5.450888      5.822042
HLX        2.087147     3.688276      3.876884      3.322389      2.898067     3.650425      3.606824
CP         6.881127     4.341357      3.822997      3.675032      3.627793     2.547273      2.958621
       AI007_P53_PRE AI007_P55_PRE AI007_P58_PRE AI007_P5_PRE
CLASP1      4.231314      3.771631      3.568651     4.006333
TSC2        5.481398      4.877598      5.269735     4.979936
ERGIC2      5.646618      5.772191      5.294558     5.661165
HLX         3.738690      2.879296      3.217329     4.466302
CP          2.451008      3.344159      2.460829     5.564000
8138 more rows ...

$weights
         [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7]     [,8]     [,9]    [,10]    [,11]
[1,] 6.132821 6.323556 6.437323 6.375542 6.375045 6.679664 5.206287 5.409930 6.138296 6.111870 5.134229
[2,] 9.072863 9.087302 9.095672 9.091149 9.091112 9.112929 9.015002 9.028571 9.073285 9.071275 9.010048
[3,] 9.434963 9.447456 9.452282 9.450240 9.450224 9.460068 9.380118 9.394638 9.435328 9.433563 9.374337
[4,] 3.547225 3.740831 3.858917 3.794548 3.794033 4.103236 2.834106 2.991010 3.552707 3.526290 2.779316
[5,] 2.382388 2.508922 2.585942 2.543968 2.543632 2.754007 1.926546 2.023283 2.385979 2.368675 1.893061
        [,12]    [,13]    [,14]    [,15]    [,16]    [,17]    [,18]    [,19]    [,20]    [,21]    [,22]
[1,] 6.179959 6.896016 5.646705 5.731130 6.562018 5.765628 5.587190 6.647784 6.033025 2.632132 5.639361
[2,] 9.076480 9.127719 9.043595 9.048770 9.104646 9.050859 9.039891 9.110701 9.066553 8.486099 9.043141
[3,] 9.438093 9.466732 9.408336 9.413053 9.456332 9.414957 9.404959 9.459063 9.429259 9.144571 9.407922
[4,] 3.594566 4.303067 3.173760 3.236299 3.990597 3.261958 3.129894 4.074121 3.462902 1.468931 3.168337
[5,] 2.413390 2.908688 2.137363 2.178452 2.671736 2.195304 2.108527 2.731585 2.327137 1.089671 2.133799
        [,23]    [,24]    [,25]    [,26]    [,27]    [,28]    [,29]    [,30]    [,31]    [,32]    [,33]
[1,] 7.039087 5.400551 5.153176 6.248899 6.491184 5.940153 6.022378 6.363891 6.570632 7.157016 6.923006
[2,] 9.137201 9.027959 9.011358 9.081713 9.099573 9.061198 9.065944 9.090290 9.136594 9.186961 9.165332
[3,] 9.471000 9.394081 9.375867 9.442620 9.454043 9.424380 9.428705 9.449852 9.400262 9.436130 9.421066
[4,] 4.437364 2.983717 2.793686 3.664402 3.915504 3.392700 3.454831 3.782474 3.696647 4.276691 4.042820
[5,] 3.013405 2.018800 1.901630 2.459028 2.622823 2.281107 2.321847 2.536092 2.841339 3.312300 3.111432
        [,34]    [,35]    [,36]    [,37]    [,38]    [,39]    [,40]    [,41]    [,42]    [,43]    [,44]
[1,] 7.233127 6.308359 5.046473 5.408590 6.096481 6.424026 5.601566 6.755853 6.739950 5.646449 3.737042
[2,] 9.195512 9.117424 9.033454 9.057927 9.101248 9.125993 9.070284 9.151407 9.150061 9.073149 8.915485
[3,] 9.442083 9.382198 9.283779 9.316388 9.364521 9.391210 9.330600 9.411359 9.410421 9.333821 9.172815
[4,] 4.373608 3.447620 2.514255 2.763415 3.253148 3.556333 2.900592 3.877982 3.862234 2.932826 1.850097
[5,] 3.395501 2.648695 1.956048 2.137802 2.498335 2.732780 2.237336 2.981687 2.969496 2.260671 1.480039
        [,45]    [,46]    [,47]    [,48]    [,49]    [,50]    [,51]    [,52]    [,53]    [,54]    [,55]
[1,] 5.764979 6.830537 6.463298 5.488770 6.507533 6.946668 6.234744 5.558846 5.142351 6.667052 7.060982
[2,] 9.080804 9.157678 9.128860 9.063125 9.132066 9.167271 9.111874 9.067593 9.039981 9.143844 9.176533
[3,] 9.342184 9.415731 9.393658 9.322365 9.396396 9.422417 9.376132 9.327504 9.292538 9.406085 9.428869
[4,] 3.018544 3.952390 3.593641 2.820133 3.635909 4.063154 3.379340 2.870027 2.577944 3.790476 4.161968
[5,] 2.322633 3.039293 2.761642 2.179000 2.794343 3.129874 2.595895 2.215190 2.002630 2.913953 3.214137
        [,56]    [,57]    [,58]    [,59]    [,60]
[1,] 6.337697 6.519827 6.722476 6.080606 5.509847
[2,] 9.119615 9.132952 9.148578 9.100300 9.064476
[3,] 9.384592 9.397153 9.409387 9.363485 9.323919
[4,] 3.475028 3.647702 3.844969 3.242165 2.835108
[5,] 2.669892 2.803467 2.956131 2.489845 2.189867
8138 more rows ...

$design
  [,1] [,2]
1    1    0
2    1    0
3    1    0
4    1    0
5    1    0
55 more rows ...
fit<- lmFit(v)
names(fit)
 [1] "coefficients"     "stdev.unscaled"   "sigma"            "df.residual"      "cov.coefficients"
 [6] "pivot"            "rank"             "Amean"            "method"           "design"          

Coding error is still being resolved

cont.matrix<- makeContrasts(PRE.svPOST.s= pre.s - post.s, levels= design)
Error in makeContrasts(PRE.svPOST.s = pre.s - post.s, levels = design) : 
  The levels must by syntactically valid names in R, see help(make.names).  Non-valid names:   post.s,  pre.s

Almost to volcano plot figure however, some coding issues are still being resolved

Multiple sequence analysis and Pathway analysis

ESR1SequenceFile<- system.file("/Users/heatherotto/Downloads/ESR1_refseq_transcript-2.fasta")
ESR1Sequences<- readAAStringSet("/Users/heatherotto/Downloads/ESR1_refseq_transcript-2.fasta")
ESR1Sequences
AAStringSet object of length 3:
    width seq                                                                               names               
[1]  6327 AGCTGGCGGAGGGCGTTCGTCCTGGGACTGCACTTGCTC...CTCAACCTATTTGATGTTCAAATAAAGAATTAAACTAAA NM_000125.4 Homo ...
[2]  7949 TGTACATTTATATTTTCTAATGAAAAGGAAATAATCTAT...CTCAACCTATTTGATGTTCAAATAAAGAATTAAACTAAA XM_009452243.3 PR...
[3]  2438 GTATTTTTCAGAATATCCTTTCTAGGTACAGTTTTTCAG...ATCACGGGGGACGCAGAGGGTTTCCCCGCCACAGTCTGA XM_015137107.2 PR...
FirstAlignment<- msa(ESR1Sequences)
use default substitution matrix
FirstAlignment
CLUSTAL 2.1  

Call:
   msa(ESR1Sequences)

MsaAAMultipleAlignment with 3 rows and 8024 columns
    aln                                                                                    names
[1] ------------------------------------------...TTCTCAACCTATTTGATGTTCAAATAAAGAATTAAACTAAA NM_000125.4 Homo ...
[2] TGTACATTTATATTTTCTAATGAAAAGGAAATAATCTATAAC...TTCTCAACCTATTTGATGTTCAAATAAAGAATTAAACTAAA XM_009452243.3 PR...
[3] ------------------------------------------...----------------------------------------- XM_015137107.2 PR...
Con ------------------------------------------...TTCTCAACCTATTTGATGTTCAAATAAAGAATTAAACTAAA Consensus 
print(FirstAlignment,  show= "complete")

MsaAAMultipleAlignment with 3 rows and 8024 columns
    aln (1..86)                                                                            names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] TGTACATTTATATTTTCTAATGAAAAGGAAATAATCTATAACCTTCAGTTCAGAATTCATTAGCTGTCCTATTTTGAGAACTGTTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus 

    aln (87..172)                                                                          names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] CTCTATGTAATTTTCGTCTCTGTATTGATGTGTAAAACTGGTTTTAACAGGTAGCTAAATGCTGTTTGAAAAGCATACTTCACCCA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus 

    aln (173..258)                                                                         names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] TTCTGGCAACTAAAATAATTGAAAGATTTAATTAATTTAGAAAAAATATTTCACTTTCAAAACACTTAAACTGTTCAGAGCATGTT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus 

    aln (259..344)                                                                         names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] ATTCAATAATCTACCTTTCACCAGAAATCATAATAAACACAATAAAAATGCTTACAGAACCCCCACAATGCGTTAGTATACACGAT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus 

    aln (345..430)                                                                         names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] TATTCCTTGTGTAAGTGAATCTTGTTGAGATTTTATGTTCAGTCAATTGAAATTAAATACTTTACATATTAACTAAAATGTGTCCT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus 

    aln (431..516)                                                                         names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] GCTCTATGTATTCTGGAGAAGTTACTCTCAGACAAATTTACATATTTAAATTATTTTATGGGCTAACTGATAAGTATAGAGAAGAC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus 

    aln (517..602)                                                                         names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] TGAAGACAGTTAAGATCATTTATTTCAAAATGTTTTAAAGTGTTGATTATTTATTTTGGTTTTCTTTCTTTCCCATGCCAGTTTTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus 

    aln (603..688)                                                                         names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] AGATGCACCTCTTACTTGGCAGCTGTTCCTCTGTACTGGGTACTGGGACAGAGAGAAATACAGTAGCAAGAGGGAGATCCTGCCTC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus 

    aln (689..774)                                                                         names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] CGCCCCATTCTACCATTCTCACTGCCAGAAAGCCAGCCTTTTTTCAAGGCTTGTAGAGAAGAAAATGCGAAAATATTTTTAAAAAC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus 

    aln (775..860)                                                                         names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] TCATTTAAAGTACCTACTGCATAAACCACACCAGACATGATGAGATATTAAAATGTCAATATTATTAAAAATTTTTAATATGATTT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus 

    aln (861..946)                                                                         names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] TACAGCCCCTTTGCTACTTTAAAATGTTTATCTTAGTGTTAAACAAACAATCAATAACCTCATAAACTTAAAAATTGCTGCAGGAA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus 

    aln (947..1032)                                                                        names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] ATACCGGACAGTTTATGGAAGGATCATATGACAGAAGGAAGGGCTGAAGAGTGTGAGAAGCTAGACCTCTGCAGGTTACCGAAGTC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus 

    aln (1033..1118)                                                                       names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] AAGAACCTCATTAATCAGTAACAAGAAGTGCAGAGCGGGCTTTTGAGTCCATGCCTGAGTAAGAAAGTCCCAAAAAACACTCACAG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con -------------------------------------------------------------------------------------- Consensus 

    aln (1119..1204)                                                                       names
[1] -------------------------------------------------------------------------------------- NM_000125.4 Homo ...
[2] AAGATATTTCCTTGCCCCTGCTTTTAGTTTAGCTGTAGCTAACTTTGGATTAACAAAATTTATGTGCTGAATGATGTTTTATTTTT XM_009452243.3 PR...
[3] ------GTATTTTTCAGAATATCCTTTCTAGGTACAGTTTTTCAGTTCTAGTGCACAGAATGGAAACTTGTTACCTGCTATACCAC XM_015137107.2 PR...
Con ------?T???TT?C??????T??T???T??G???????T??C??T???????CA?A???T?????CT???T??????T??????? Consensus 

    aln (1205..1290)                                                                       names
[1] -----------------------------------------------------------AGCTG---------------------- NM_000125.4 Homo ...
[2] TTTTCCAACTCCACATGCCTGTCTAGACTTCAAGCTTTATTATGAATAAAGAGAAAATCGGCTGGATGGCATAAAAAATATTTCAG XM_009452243.3 PR...
[3] ATTTTCACTAGGATGTGATGTATTTATCACAAACAACAGTATTGGTCAACATTTTCCCTCGCTGTGAAGTGCACATTTGACATCCT XM_015137107.2 PR...
Con ?TTT?CA?????A??TG??????T???C???AA??????T??TG???AA???????????GCTG????G???A?A????A??TC?? Consensus 

    aln (1291..1376)                                                                       names
[1] -----------------------------------------------------------------------GCGGAGGGCGTTCGT NM_000125.4 Homo ...
[2] GCAGATTAACACATGATT--------------------TACCTCTTCTTGAACATCCATCTTAATGGAAGTGCTAAGAAAGTTAGA XM_009452243.3 PR...
[3] TTAGAAAAATTACTGACGGTTTTGAGACGATTGTTTTGTGCTTTCTTTCAGTCAACGTAATTTTCCCGAAAGCAGAGATGACTCTT XM_015137107.2 PR...
Con ??AGA??AA????TGA??--------------------T?C?T??T?T????CA?C????TT??????A??GC?GAGA??GTTCGT Consensus 

    aln (1377..1462)                                                                       names
[1] CCTGG------------GACTG------------------CACTTGCTCC------------------------------------ NM_000125.4 Homo ...
[2] TTCGG------------GCCTGGCTTGGCAAAAGCAAGGCCACCCCCTCCTCTATTTTTTCAATGAGATTTTCCAATCCTAGTCAA XM_009452243.3 PR...
[3] CCAGACATGCTAACAATGCCTG-----AACAAACTGTGTAAGCTTAGTCCAAAAAAAATATTTG---------------------- XM_015137107.2 PR...
Con CC?GG------------GCCTG-----???AAA????G??CACTT?CTCC???A????T?????---------------------- Consensus 

    aln (1463..1548)                                                                       names
[1] -------------------------------------------------------------CGTCGGG-------TCGCCCGGCTT NM_000125.4 Homo ...
[2] ATGGTGGTGCTAGTTCTTTATTTTTGAGTTACTGCATTTCCTAATTTCATGGTCGTAACAGCCTCCTG-------TCTACCGACTC XM_009452243.3 PR...
[3] ---------------------ATTAATAGATTTTATTTTGGTAGATTCTAAGGTTCTAAGCAGTCAGAGAAATAATCGCAGAGCCT XM_015137107.2 PR...
Con ---------------------?TT????????T???TTT??TA??TTC???G?????A???CGTC?GG-------TCGCCCGGCTT Consensus 

    aln (1549..1634)                                                                       names
[1] C--------------------ACCGGACCCGCAG--------------------GCTCCCGGGGCAGGG---------CCGGGGC- NM_000125.4 Homo ...
[2] AGAACGGATTTTACCAAA---ACTGAAAATGCAG--------------------GCTCCATGCTCAGAAGCTCTTTAACAGGCTC- XM_009452243.3 PR...
[3] CAAATATCTCCAAAATCTGATACCAATCCCTTTGATTGTGAATTATATTCTGTAGCTACCAAAGAAGGGAGAAGAAAACTAGGAAG XM_015137107.2 PR...
Con C?AA????T???A?????---ACCGAACCCGCAG--------------------GCTCCC?G?GCAGGG???????AAC?GGG?C- Consensus 

    aln (1635..1720)                                                                       names
[1] ---------CAGAG-----CTCGCGTGTCGGCGGGACATGCGCTG-----------------------------CGTCGCCTCTA- NM_000125.4 Homo ...
[2] ---------GAAAGGTCCATGCTCCTTTCTCCTGCCCATTCTATAGCATAAGAAGACAGTCTCTGAGTGATAATCTTCTCTTCAAG XM_009452243.3 PR...
[3] GAGTAAGCACAAAGATCTCTTCACGT-TCTCCGGAACTGTAGTAGCAAATAGCAG-----------------CACGGCGCTTCTTG XM_015137107.2 PR...
Con ---------CAAAG?TC??TTC?CGT?TCTCCGG?ACATTCG?TG??A??AG?AG-----------------??CGTCGCTTCTAG Consensus 

    aln (1721..1806)                                                                       names
[1] --------------------------ACCTCGGGCTGTGCTCTTTTTCCAG----------------------------------- NM_000125.4 Homo ...
[2] AAGAAGAAAACTAGGAAGGAGTAAGCACAAAGATCTCTTCACATTCTCTGGGACTGCGGTACCAAATATCAGCACAGCACTTCTTG XM_009452243.3 PR...
[3] AAAAAGG---------------ATGTAGATTTTAATCTGAACTTTGAACCG----------------------------------- XM_015137107.2 PR...
Con AA?AAG?---------------A?G?ACAT?G??CTCTGCACTTT?TCC?G----------------------------------- Consensus 

    aln (1807..1892)                                                                       names
[1] --------------------------------------------GTGGCCCGCCGGTTTCTGAGCCTTCTGCCCTGCGGGGACACG NM_000125.4 Homo ...
[2] AAAAAGGATGTAGATTTTAATCTGAACTTTGAACCATCACTGAGGTGGCCCGCCGGCTTCTGAGCCTTCTGCCCTGCGGGGACACG XM_009452243.3 PR...
[3] ------------------------------------TCATTGAGGTGGCCCGCCGGCTTCTGAGCCTTCTGCCCTGCGGGGACACG XM_015137107.2 PR...
Con ------------------------------------TCA?TGAGGTGGCCCGCCGGCTTCTGAGCCTTCTGCCCTGCGGGGACACG Consensus 

    aln (1893..1978)                                                                       names
[1] GTCTGCACCCTGCCCGCGGCCACGGACCATGACCATGACCCTCCACACCAAAGCATCTGGGATGGCCCTACTGCATCAGATCCAAG NM_000125.4 Homo ...
[2] GTCTGCACCCTGCCCGCGGCCACGGACCATGACCATGACCCTCCACACCAAAGCATCCGGGATGGCCCTACTGCATCAGATCCAAG XM_009452243.3 PR...
[3] GTCTGCGCCCTGCCCACGGCCACGGACCATGACCATGACCCTCCACACCAAAGCATCCGGGATGGCCCTACTGCATCAGATCCAAG XM_015137107.2 PR...
Con GTCTGCACCCTGCCCGCGGCCACGGACCATGACCATGACCCTCCACACCAAAGCATCCGGGATGGCCCTACTGCATCAGATCCAAG Consensus 

    aln (1979..2064)                                                                       names
[1] GGAACGAGCTGGAGCCCCTGAACCGTCCGCAGCTCAAGATCCCCCTGGAGCGGCCCCTGGGCGAGGTGTACCTGGACAGCAGCAAG NM_000125.4 Homo ...
[2] GGAACGAGCTGGAGCCCCTGAACCGTCCGCAGCTCAAGATCCCCCTGGAGCGGCCCCTGGGCGAGGTGTACGTGGACAGCAGCAAG XM_009452243.3 PR...
[3] GGAACGAGCTGGAGCCCCTGAACCGTCCGCAGCTCAAGATCCCCCTGGAGCGGCCCCTGGGCGAGGTGTACGTGGACAGCAGCAAG XM_015137107.2 PR...
Con GGAACGAGCTGGAGCCCCTGAACCGTCCGCAGCTCAAGATCCCCCTGGAGCGGCCCCTGGGCGAGGTGTACGTGGACAGCAGCAAG Consensus 

    aln (2065..2150)                                                                       names
[1] CCCGCCGTGTACAACTACCCCGAGGGCGCCGCCTACGAGTTCAACGCCGCGGCCGCCGCCAACGCGCAGGTCTACGGTCAGACCGG NM_000125.4 Homo ...
[2] CCCGCCGTGTACAACTACCCCGAGGGCGCCGCCTACGAGTTCAACGCCGCGGCCGCGGCCAACGCGCAGGTCTACGGTCAGACCGG XM_009452243.3 PR...
[3] CCCGCCGTGTACAACTACCCCGAGGGCGCCGCCTACGAGTTCAACGCCGCGGCCGCCGCCAACGCGCAGGTCTACGGCCAGACTGG XM_015137107.2 PR...
Con CCCGCCGTGTACAACTACCCCGAGGGCGCCGCCTACGAGTTCAACGCCGCGGCCGCCGCCAACGCGCAGGTCTACGGTCAGACCGG Consensus 

    aln (2151..2236)                                                                       names
[1] CCTCCCCTACGGCCCCGGGTCTGAGGCTGCGGCGTTCGGCTCCAACGGCCTGGGGGGTTTCCCCCCACTCAACAGCGTGTCTCCGA NM_000125.4 Homo ...
[2] CCTCCCCTACGGCCCCGGGTCTGAGGCTGCGGCGTTCGGCTCCAACGGCCTCGGGGGTTTCCCCCCACTCAACAGCGTGTCTCCGA XM_009452243.3 PR...
[3] CCTCCCGTACGGCCCCGGGTCTGAGGCTGCGGCGTTCGGCTCCAACGGCCTGGGGGGTTTCCCCCCACTCAACAGCGTGTCTCCGA XM_015137107.2 PR...
Con CCTCCCCTACGGCCCCGGGTCTGAGGCTGCGGCGTTCGGCTCCAACGGCCTGGGGGGTTTCCCCCCACTCAACAGCGTGTCTCCGA Consensus 

    aln (2237..2322)                                                                       names
[1] GCCCGCTGATGCTACTGCACCCGCCGCCGCAGCTGTCGCCTTTCCTGCAGCCCCACGGCCAGCAGGTGCCCTACTACCTGGAGAAC NM_000125.4 Homo ...
[2] GCCCGCTGATGCTACTGCACCCGCCGCCGCAGCTGTCGCCTTTCCTGCAGCCCCACGGCCAGCAGGTGCCCTACTACCTGGAGAAC XM_009452243.3 PR...
[3] GCCCGCTGATGCTGCTGCACCCGCCGCCGCAGCTGTCGCCTTTCCTGCAGCCCCACGGCCAGCAGGTGCCCTACTACCTGGAGAAC XM_015137107.2 PR...
Con GCCCGCTGATGCTACTGCACCCGCCGCCGCAGCTGTCGCCTTTCCTGCAGCCCCACGGCCAGCAGGTGCCCTACTACCTGGAGAAC Consensus 

    aln (2323..2408)                                                                       names
[1] GAGCCCAGCGGCTACACGGTGCGCGAGGCCGGCCCGCCGGCATTCTACAGGCCAAATTCAGATAATCGACGCCAGGGTGGCAGAGA NM_000125.4 Homo ...
[2] GAGCCCAGCGGCTACACGGTGCGCGAGGCCGGCCCGCCGGCATTCTACAGGCCAAATTCAGATAATCGACGCCAGGGTGGCAGAGA XM_009452243.3 PR...
[3] GAGCCCAGCGGCTACACGGTGCGCGAGGCCGGCCCTCCGGCATTCTACAGGCCAAATTCAGATAATCGACGCCAGGGTGGCAGAGA XM_015137107.2 PR...
Con GAGCCCAGCGGCTACACGGTGCGCGAGGCCGGCCCGCCGGCATTCTACAGGCCAAATTCAGATAATCGACGCCAGGGTGGCAGAGA Consensus 

    aln (2409..2494)                                                                       names
[1] AAGATTGGCCAGTACCAATGACAAGGGAAGTATGGCTATGGAATCTGCCAAGGAGACTCGCTACTGTGCAGTGTGCAATGACTATG NM_000125.4 Homo ...
[2] AAGATTGGCCAGTACCAATGACAAGGGAAGTATGGCTATGGAATCTGCCAAGGAGACTCGCTACTGTGCAGTGTGCAATGACTATG XM_009452243.3 PR...
[3] GAGATTGGCCAGTACCAATGACAAGGGAAGTATGGCTATGGAATCTGCCAAGGAGACTCGCTACTGTGCAGTGTGCAATGACTATG XM_015137107.2 PR...
Con AAGATTGGCCAGTACCAATGACAAGGGAAGTATGGCTATGGAATCTGCCAAGGAGACTCGCTACTGTGCAGTGTGCAATGACTATG Consensus 

    aln (2495..2580)                                                                       names
[1] CTTCAGGCTACCATTATGGAGTCTGGTCCTGTGAGGGCTGCAAGGCCTTCTTCAAGAGAAGTATTCAAG------GACATAACGAC NM_000125.4 Homo ...
[2] CTTCAGGCTACCATTATGGAGTCTGGTCCTGTGAGGGCTGCAAGGCCTTCTTCAAGAGAAGTATTCAAGGTAATAGACATAACGAC XM_009452243.3 PR...
[3] CTTCAGGCTACCATTATGGAGTCTGGTCCTGTGAGGGCTGCAAGGCCTTCTTCAAGAGAAGTATTCAAGGTAATAGACATAACGAC XM_015137107.2 PR...
Con CTTCAGGCTACCATTATGGAGTCTGGTCCTGTGAGGGCTGCAAGGCCTTCTTCAAGAGAAGTATTCAAGGTAATAGACATAACGAC Consensus 

    aln (2581..2666)                                                                       names
[1] TATATGTGTCCAGCCACCAACCAGTGCACCATTGATAAAAACAGGAGGAAGAGCTGCCAGGCCTGCCGGCTCCGTAAATGCTACGA NM_000125.4 Homo ...
[2] TATATGTGTCCAGCCACCAACCAGTGCACCATTGATAAAAACAGGAGGAAGAGCTGCCAGGCCTGCCGGCTCCGCAAATGCTACGA XM_009452243.3 PR...
[3] TATATGTGTCCAGCCACCAACCAGTGCACCATTGATAAGAACAGGAGGAAGAGCTGCCAGGCCTGCCGGCTCCGCAAATGCTACGA XM_015137107.2 PR...
Con TATATGTGTCCAGCCACCAACCAGTGCACCATTGATAAAAACAGGAGGAAGAGCTGCCAGGCCTGCCGGCTCCGCAAATGCTACGA Consensus 

    aln (2667..2752)                                                                       names
[1] AGTGGGAATGATGAAAGGTGGGATACGAAAAGACCGAAGAGGAGGGAGAATGTTGAAACACAAGCGCCAGAGAGATGATGGGGAGG NM_000125.4 Homo ...
[2] AGTGGGAATGATGAAAGGTGGGATACGAAAAGACCGAAGAGGAGGGAGAATGTTGAAACACAAGCGCCAGAGAGATGATGGGGAGG XM_009452243.3 PR...
[3] AGTGGGAATGATGAAAGGTGGGATACGAAAAGACCGAAGAGGAGGGAGAATGTTGAAACACAAGCGCCAGAGAGATGATGGGGAGG XM_015137107.2 PR...
Con AGTGGGAATGATGAAAGGTGGGATACGAAAAGACCGAAGAGGAGGGAGAATGTTGAAACACAAGCGCCAGAGAGATGATGGGGAGG Consensus 

    aln (2753..2838)                                                                       names
[1] GCAGGGGTGAAGTGGGGTCTGCTGGAGACATGAGAGCTGCCAACCTTTGGCCAAGCCCGCTCATGATCAAACGCTCTAAGAAGAAC NM_000125.4 Homo ...
[2] GCAGGGGTGAAGTGGGGTCTGCTGGAGACATGAGAGCTGCCAACCTTTGGCCAAGCCCGCTCATGATCAAACACTCTAAGAAGAAC XM_009452243.3 PR...
[3] GCAGGGGTGAAGTGGGGTCCGCTGGAGACATGAGAGCTGCCAACCTTTGGCCAAGCCCGCTCATGATCAAGCACTCTAAGAAGAAC XM_015137107.2 PR...
Con GCAGGGGTGAAGTGGGGTCTGCTGGAGACATGAGAGCTGCCAACCTTTGGCCAAGCCCGCTCATGATCAAACACTCTAAGAAGAAC Consensus 

    aln (2839..2924)                                                                       names
[1] AGCCTGGCCTTGTCCCTGACGGCCGACCAGATGGTCAGTGCCTTGTTGGATGCTGAGCCCCCGATACTCTATTCCGAGTATGATCC NM_000125.4 Homo ...
[2] AGCCCGGCCTTGTCCCTGACGGCCGACCAGATGGTCAGTGCCTTGTTGGATGCTGAGCCCCCCATACTCTATTCCGAGTATGATCC XM_009452243.3 PR...
[3] AGCCCGGCCTTGTCCCTGACGGCCGACCAGATGGTCAGTGCCTTGCTGGATGCTGAGCCCCCTATACTCTATTCCGAGTATGATCC XM_015137107.2 PR...
Con AGCCCGGCCTTGTCCCTGACGGCCGACCAGATGGTCAGTGCCTTGTTGGATGCTGAGCCCCC?ATACTCTATTCCGAGTATGATCC Consensus 

    aln (2925..3010)                                                                       names
[1] TACCAGACCCTTCAGTGAAGCTTCGATGATGGGCTTACTGACCAACCTGGCAGACAGGGAGCTGGTTCACATGATCAACTGGGCGA NM_000125.4 Homo ...
[2] TACCAGACCCTTCAGTGAGGCTTCGATGATGGGCTTACTGACCAACCTGGCAGACAGGGAGCTGGTTCACATGATCAACTGGGCAA XM_009452243.3 PR...
[3] TACCAGACCCTTCAGTGAAGCTTCGATGATGGGCTTACTGACCAACCTGGCAGACAGGGAGCTGGTTCACATGATCAACTGGGCAA XM_015137107.2 PR...
Con TACCAGACCCTTCAGTGAAGCTTCGATGATGGGCTTACTGACCAACCTGGCAGACAGGGAGCTGGTTCACATGATCAACTGGGCAA Consensus 

    aln (3011..3096)                                                                       names
[1] AGAGGGTGCCAGGCTTTGTGGATTTGACCCTCCATGATCAGGTCCACCTTCTAGAATGTGCCTGGCTAGAGATCCTGATGATTGGT NM_000125.4 Homo ...
[2] AGAGGGTGCCAGGCTTTGTGGATTTGACCCTCCATGATCAGGTCCACCTTCTAGAATGTGCCTGGCTAGAGATCCTGATGATTGGT XM_009452243.3 PR...
[3] AGAGGGTGCCAGGCTTTGTGGATTTGACCCTCCATGATCAGGTCCACCTTCTAGAATGTGCCTGGCTAGAGATCCTGATGATTGGT XM_015137107.2 PR...
Con AGAGGGTGCCAGGCTTTGTGGATTTGACCCTCCATGATCAGGTCCACCTTCTAGAATGTGCCTGGCTAGAGATCCTGATGATTGGT Consensus 

    aln (3097..3182)                                                                       names
[1] CTCGTCTGGCGCTCCATGGAGCACCCAGGGAAGCTACTGTTTGCTCCTAACTTGCTCTTGGACAGGAACCAGGGAAAATGTGTAGA NM_000125.4 Homo ...
[2] CTCGTCTGGCGCTCCATGGAGCACCCAGGGAAGCTCCTGTTTGCTCCTAACTTGCTCTTGGACAGGAACCAGGGAAAATGTGTAGA XM_009452243.3 PR...
[3] CTCGTCTGGCGCTCCATGGAGCACCCAGGGAAGCTCCTGTTTGCTCCTAACTTGCTCTTGGACAGGAACCAGGGAAAATGTGTAGA XM_015137107.2 PR...
Con CTCGTCTGGCGCTCCATGGAGCACCCAGGGAAGCTCCTGTTTGCTCCTAACTTGCTCTTGGACAGGAACCAGGGAAAATGTGTAGA Consensus 

    aln (3183..3268)                                                                       names
[1] GGGCATGGTGGAGATCTTCGACATGCTGCTGGCTACATCATCTCGGTTCCGCATGATGAATCTGCAGGGAGAGGAGTTTGTGTGCC NM_000125.4 Homo ...
[2] GGGCATGGTGGAGATCTTCGACATGCTGCTGGCTACATCATCTCGGTTCCGCATGATGAATCTGCAGGGAGAGGAGTTTGTGTGCC XM_009452243.3 PR...
[3] GGGCATGGTGGAGATCTTCGACATGTTACTGGCCACATCATCTCGGTTCCGCATGATGAATCTGCAGGGAGAGGAGTTTGTGTGCC XM_015137107.2 PR...
Con GGGCATGGTGGAGATCTTCGACATGCTGCTGGCTACATCATCTCGGTTCCGCATGATGAATCTGCAGGGAGAGGAGTTTGTGTGCC Consensus 

    aln (3269..3354)                                                                       names
[1] TCAAATCTATTATTTTGCTTAATTCTGGAGTGTACACATTTCTGTCCAGCACCCTGAAGTCTCTGGAAGAGAAGGACCATATCCAC NM_000125.4 Homo ...
[2] TCAAGTCTATTATTTTGCTTAATTCTGGAGTGTACACATTTCTGTCCAGCACCCTGAAGTCTCTGGAAGAGAAGGACCATATCCAC XM_009452243.3 PR...
[3] TCAAATCTATTATTTTGCTTAATTCTGGAGTGTACACATTTCTGTCCAGCACCCTGAAGTCTCTGGAAGAGAAGGACCATATCCAC XM_015137107.2 PR...
Con TCAAATCTATTATTTTGCTTAATTCTGGAGTGTACACATTTCTGTCCAGCACCCTGAAGTCTCTGGAAGAGAAGGACCATATCCAC Consensus 

    aln (3355..3440)                                                                       names
[1] CGAGTCCTGGACAAGATCACAGACACTTTGATCCACCTGATGGCCAAGGCAGGCCTGACCCTGCAGCAGCAGCACCAGCGGCTGGC NM_000125.4 Homo ...
[2] CGAGTCCTGGACAAGATCACAGACACTTTGATCCACCTGATGGCCAAGGCAGGCCTGACCCTGCAGCAGCAGCACCGGCGGCTGGC XM_009452243.3 PR...
[3] CGAGTCCTGGACAAGATCACAGACACTTTGATCCACCTGATGGCCAAGGCAGGCCTGACCCTGCAGCAGCAGCACCGGCGGCTGGC XM_015137107.2 PR...
Con CGAGTCCTGGACAAGATCACAGACACTTTGATCCACCTGATGGCCAAGGCAGGCCTGACCCTGCAGCAGCAGCACCGGCGGCTGGC Consensus 

    aln (3441..3526)                                                                       names
[1] CCAGCTCCTCCTCATCCTCTCCCACATCAGGCACATGAGTAACAAAGGCATGGAGCATCTGTACAGCATGAAGTGCAAGAACGTGG NM_000125.4 Homo ...
[2] CCAGCTCCTCCTCATCCTCTCCCACATCAGGCACATGAGTAACAAAGGCATGGAGCATCTGTACAGCATGAAGTGCAAGAACGTGG XM_009452243.3 PR...
[3] CCAGCTCCTCCTCATCCTCTCCCACATCAGGCACATGAGTAACAAAGGCATGGAGCATCTGTACAGCATGAAGTGCAAGAATGTGG XM_015137107.2 PR...
Con CCAGCTCCTCCTCATCCTCTCCCACATCAGGCACATGAGTAACAAAGGCATGGAGCATCTGTACAGCATGAAGTGCAAGAACGTGG Consensus 

    aln (3527..3612)                                                                       names
[1] TGCCCCTCTATGACCTGCTGCTGGAGATGCTGGACGCCCACCGCCTACATGCGCCCACTAGCCGTGGAGGGGCATCCGTGGAGGAG NM_000125.4 Homo ...
[2] TGCCCCTCTATGACCTGCTGCTGGAGATGCTGGACGCCCACCGCCTACATGCGCCCACTAGCCGTGGAGGGGCGCCCGTGGAGGAG XM_009452243.3 PR...
[3] TGCCCCTCTACGACCTGCTGCTGGAGATGCTGGACGCCCACCGCCTACATGCGCCCACTAGCCGTGGAGGGGCGCCCATGGAGGAG XM_015137107.2 PR...
Con TGCCCCTCTATGACCTGCTGCTGGAGATGCTGGACGCCCACCGCCTACATGCGCCCACTAGCCGTGGAGGGGCGCCCGTGGAGGAG Consensus 

    aln (3613..3698)                                                                       names
[1] ACGGACCAAAGCCACTTGGCCACTGCGGGCTCTACTTCATCGCATTCCTTGCAAAAGTATTACATCACGGGGGAGGCAGAGGGTTT NM_000125.4 Homo ...
[2] ACGGACCAAAGCCACTTGGCCACTGCGGGCTCTACTTCATCGCATTCCTTGCAAAAGTATTACATCACGGGGGAGGCAGAGGGTTT XM_009452243.3 PR...
[3] ACGGACCAAAGCCACTTGGCCACCGCGGGCTCTACTTCATCGCATTCCTTGCAAAAGTATTACATCACGGGGGACGCAGAGGGTTT XM_015137107.2 PR...
Con ACGGACCAAAGCCACTTGGCCACTGCGGGCTCTACTTCATCGCATTCCTTGCAAAAGTATTACATCACGGGGGAGGCAGAGGGTTT Consensus 

    aln (3699..3784)                                                                       names
[1] CCCTGCCACGGTCTGAGAGCTCCCTGGCTCCCACACGGTTCAGATAATCCCTGCTGCATTTTACCCTCATCATGCACCACTTTAGC NM_000125.4 Homo ...
[2] CCCTGCCACAGTCTGAGAGTTCCCTGGCTCCCACACGGTTCAGATAATCCCTGCTGCATTTTACCCTCATCATGCACCACTTTAGC XM_009452243.3 PR...
[3] CCCCGCCACAGTCTGA---------------------------------------------------------------------- XM_015137107.2 PR...
Con CCCTGCCACAGTCTGAGAG?TCCCTGGCTCCCACACGGTTCAGATAATCCCTGCTGCATTTTACCCTCATCATGCACCACTTTAGC Consensus 

    aln (3785..3870)                                                                       names
[1] CAAATTCTGTCTCCTGCATACACTCCGGCATGCATCCAACACCAATGGCTTTCTAGATGAGTGGCCATTCATTTGCTTGCTCAGTT NM_000125.4 Homo ...
[2] CAAATTCTGTCTCCTGCATACACTCCGGCATGCATCCAACACCAATGGCTTTCTAGATGAGTGGCCATTCATTTGCTTGCTCAGTT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CAAATTCTGTCTCCTGCATACACTCCGGCATGCATCCAACACCAATGGCTTTCTAGATGAGTGGCCATTCATTTGCTTGCTCAGTT Consensus 

    aln (3871..3956)                                                                       names
[1] CTTAGTGGCACATCTTCTGTCTTCTGTTGGGAACAGCCAAAGGGATTCCAAGGCTAAATCTTTGTAACAGCTCTCTTTCCCCCTTG NM_000125.4 Homo ...
[2] CTTAGTGGCACATCTTCTGTCTTCTGTTGGGAACAGCCAAAGGGATTCCAAGGCTAAATCTTTGTAACAGCTCTCTTTCCCCCTTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CTTAGTGGCACATCTTCTGTCTTCTGTTGGGAACAGCCAAAGGGATTCCAAGGCTAAATCTTTGTAACAGCTCTCTTTCCCCCTTG Consensus 

    aln (3957..4042)                                                                       names
[1] CTATGTTACTAAGCGTGAGGATTCCCGTAGCTCTTCACAGCTGAACTCAGTCTATGGGTTGGGGCTCAGATAACTCTGTGCATTTA NM_000125.4 Homo ...
[2] CTATGTTACTAAGCGTGAGGATTCCCGTAGCTCTTCACAGCTGAACTCAGTCTATGGGTTGGGGCTCAGATAACTCTGTGCATTTA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CTATGTTACTAAGCGTGAGGATTCCCGTAGCTCTTCACAGCTGAACTCAGTCTATGGGTTGGGGCTCAGATAACTCTGTGCATTTA Consensus 

    aln (4043..4128)                                                                       names
[1] AGCTACTTGTAGAGACCCAGGCCTGGAGAGTAGACATTTTGCCTCTGATAAGCACTTTTTAAATGGCTCTAAGAATAAGCCACAGC NM_000125.4 Homo ...
[2] AGCTACTTGTAGAGACCCAGGCCTGGAGAGTAGACATTTTGCCTCTGATAAGCACTTTTTAAATGGCTCTAAGAATAAGCCACAGC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AGCTACTTGTAGAGACCCAGGCCTGGAGAGTAGACATTTTGCCTCTGATAAGCACTTTTTAAATGGCTCTAAGAATAAGCCACAGC Consensus 

    aln (4129..4214)                                                                       names
[1] AAAGAATTTAAAGTGGCTCCTTTAATTGGTGACTTGGAGAAAGCTAGGTCAAGGGTTTATTATAGCACCCTCTTGTATTCCTATGG NM_000125.4 Homo ...
[2] AAAGAATTTAAAGTGGCTCCTTTAATTGGTGACTTGGAGAAAGCTAGGTCAAGGGTTTATTATAGCACCCTCTTGTATTCCTATGG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AAAGAATTTAAAGTGGCTCCTTTAATTGGTGACTTGGAGAAAGCTAGGTCAAGGGTTTATTATAGCACCCTCTTGTATTCCTATGG Consensus 

    aln (4215..4300)                                                                       names
[1] CAATGCATCCTTTTATGAAAGTGGTACACCTTAAAGCTTTTATATGACTGTAGCAGAGTATCTGGTGATTGTCAATTCATTCCCCC NM_000125.4 Homo ...
[2] CAATGCATCCTTTTATGAAAGTGGTACACCTTAAAGCTTTTATATGACTGTAGCAGAGTATCTGGTGATTGTCAATTCATTCCCCC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CAATGCATCCTTTTATGAAAGTGGTACACCTTAAAGCTTTTATATGACTGTAGCAGAGTATCTGGTGATTGTCAATTCATTCCCCC Consensus 

    aln (4301..4386)                                                                       names
[1] TATAGGAATACAAGGGGCACACAGGGAAGGCAGATCCCCTAGTTGGCAAGACTATTTTAACTTGATACACTGCAGATTCAGATGTG NM_000125.4 Homo ...
[2] TATAGGAATACAAGGGGCACACAGGGAAGGCAGATCCCCTAGTTGGCAAGACTATTTTAACTTGATACACTGCAGCTTCAGATGTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TATAGGAATACAAGGGGCACACAGGGAAGGCAGATCCCCTAGTTGGCAAGACTATTTTAACTTGATACACTGCAG?TTCAGATGTG Consensus 

    aln (4387..4472)                                                                       names
[1] CTGAAAGCTCTGCCTCTGGCTTTCCGGTCATGGGTTCCAGTTAATTCATGCCTCCCATGGACCTATGGAGAGCAGCAAGTTGATCT NM_000125.4 Homo ...
[2] CTGAAAGCTCTGCCTCTGGCTTTCCGGTCATGGGTTCCAGTTAATTCATGCCTCCCATGGACCTATGGAGAGCAGCAAGTTGATCT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CTGAAAGCTCTGCCTCTGGCTTTCCGGTCATGGGTTCCAGTTAATTCATGCCTCCCATGGACCTATGGAGAGCAGCAAGTTGATCT Consensus 

    aln (4473..4558)                                                                       names
[1] TAGTTAAGTCTCCCTATATGAGGGATAAGTTCCTGATTTTTGTTTTTATTTTTGTGTTACAAAAGAAAGCCCTCCCTCCCTGAACT NM_000125.4 Homo ...
[2] TAGTTAAGTCTCCCTATATGAGGGATAAGTTCCTGATTTTTGTTTTTATTTTTGTGTTACAAAAGAAAGCCCTCCCTCCCTGAACT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TAGTTAAGTCTCCCTATATGAGGGATAAGTTCCTGATTTTTGTTTTTATTTTTGTGTTACAAAAGAAAGCCCTCCCTCCCTGAACT Consensus 

    aln (4559..4644)                                                                       names
[1] TGCAGTAAGGTCAGCTTCAGGACCTGTTCCAGTGGGCACTGTACTTGGATCTTCCCGGCGTGTGTGTGCCTTACACAGGGGTGAAC NM_000125.4 Homo ...
[2] TGCAGTAAGGTCAGCTTCAGGACCTGTTCCAGTGGGCACTGTACTTGGATCTTCCCGGCGTGTGTGTGCCTTACACAGGGGTGAAC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TGCAGTAAGGTCAGCTTCAGGACCTGTTCCAGTGGGCACTGTACTTGGATCTTCCCGGCGTGTGTGTGCCTTACACAGGGGTGAAC Consensus 

    aln (4645..4730)                                                                       names
[1] TGTTCACTGTGGTGATGCATGATGAGGGTAAATGGTAGTTGAAAGGAGCAGGGGCCCTGGTGTTGCATTTAGCCCTGGGGCATGGA NM_000125.4 Homo ...
[2] TGTTCACTGTGGTGATGCATGATGAGAGTAAATGGTAGTTGAAAGGAGCAGGGGCCCTGGTGTTGCATTGAGCCCTGGGGCATGGA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TGTTCACTGTGGTGATGCATGATGAG?GTAAATGGTAGTTGAAAGGAGCAGGGGCCCTGGTGTTGCATT?AGCCCTGGGGCATGGA Consensus 

    aln (4731..4816)                                                                       names
[1] GCTGAACAGTACTTGTGCAGGATTGTTGTGGCTACTAGAGAACAAGAGGGAAAGTAGGGCAGAAACTGGATACAGTTCTGAGGCAC NM_000125.4 Homo ...
[2] GCTGAACAGTACTTGTGCAGGATTGTTGTGGCTACTAGAGAACAAGAGGGAAAGTAGGGCAGAAACTGGATACAGTTCTGAGGCAC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con GCTGAACAGTACTTGTGCAGGATTGTTGTGGCTACTAGAGAACAAGAGGGAAAGTAGGGCAGAAACTGGATACAGTTCTGAGGCAC Consensus 

    aln (4817..4902)                                                                       names
[1] AGCCAGACTTGCTCAGGGTGGCCCTGCCACAGGCTGCAGCTACCTAGGAACATTCCTTGCAGACCCCGCATTGCCCTTTGGGGGTG NM_000125.4 Homo ...
[2] AGCCAGACTTGCTCAGGGTGGCCCTGCCACAGGCTGCAGCTACCTAGGAACATTCCTTGCAGACCCCGCATTGCCCTTTGGGGGTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AGCCAGACTTGCTCAGGGTGGCCCTGCCACAGGCTGCAGCTACCTAGGAACATTCCTTGCAGACCCCGCATTGCCCTTTGGGGGTG Consensus 

    aln (4903..4988)                                                                       names
[1] CCCTGGGATCCCTGGGGTAGTCCAGCTCTTCTTCATTTCCCAGCGTGGCCCTGGTTGGAAGAAGCAGCTGTCACAGCTGCTGTAGA NM_000125.4 Homo ...
[2] CCCTGGGATCCCTGGGGTAGTCCAGCTCTTCTTCATTTCCCAGCGTGGCCCTGGTTGGAAGAAGCAGCTGTCACAGCTGCTGTAGA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CCCTGGGATCCCTGGGGTAGTCCAGCTCTTCTTCATTTCCCAGCGTGGCCCTGGTTGGAAGAAGCAGCTGTCACAGCTGCTGTAGA Consensus 

    aln (4989..5074)                                                                       names
[1] CAGCTGTGTTCCTACAATTGGCCCAGCACCCTGGGGCACGGGAGAAGGGTGGGGACCGTTGCTGTCACTACTCAGGCTGACTGGGG NM_000125.4 Homo ...
[2] CAGCTGTGTTCCTACAATTGGCCCAGCACCCTGGGGCACGGGAGAAGGGTGGGGACCGTTGCTGTCACTACTCAGGCTGACTGGGG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CAGCTGTGTTCCTACAATTGGCCCAGCACCCTGGGGCACGGGAGAAGGGTGGGGACCGTTGCTGTCACTACTCAGGCTGACTGGGG Consensus 

    aln (5075..5160)                                                                       names
[1] CCTGGTCAGATTACGTATGCCCTTGGTGGTTTAGAGATAATCCAAAATCAGGGTTTGGTTTGGGGAAGAAAATCCTCCCCCTTCCT NM_000125.4 Homo ...
[2] CCTGGTCAGATTACCTATGCCCTTGGTGGTTTAGAGCTAATCCAAAATCAGGGTTTGGTTTGGGGAAGAAAATCCTCCCCCTTCCT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CCTGGTCAGATTAC?TATGCCCTTGGTGGTTTAGAG?TAATCCAAAATCAGGGTTTGGTTTGGGGAAGAAAATCCTCCCCCTTCCT Consensus 

    aln (5161..5246)                                                                       names
[1] CCCCCGCCCCGTTCCCTACCGCCTCCACTCCTGCCAGCTCATTTCCTTCAATTTCCTTTGACCTATAGGCTAAAAAAGAAAGGCTC NM_000125.4 Homo ...
[2] CCCCCGCCCCGTTCCCTACCGCCTCCACTCCTGCCAGCTCATTTCCTTCAATTTCCTTTGACCTATAGGCTAAAAAAGAAAGGCTC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CCCCCGCCCCGTTCCCTACCGCCTCCACTCCTGCCAGCTCATTTCCTTCAATTTCCTTTGACCTATAGGCTAAAAAAGAAAGGCTC Consensus 

    aln (5247..5332)                                                                       names
[1] ATTCCAGCCACAGGGCAGCCTTCCCTGGGCCTTTGCTTCTCTAGCACAATTATGGGTTACTTCCTTTTTCTTAACAAAAAAGAATG NM_000125.4 Homo ...
[2] ATTCCAGCCACAGGGCAGCCTTCCCTGGGCCTTTGCTTCTCTAGCACAATTATGGGTTACTTCCTTTTTCTTAACAAAAAAGAATG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con ATTCCAGCCACAGGGCAGCCTTCCCTGGGCCTTTGCTTCTCTAGCACAATTATGGGTTACTTCCTTTTTCTTAACAAAAAAGAATG Consensus 

    aln (5333..5418)                                                                       names
[1] TTTGATTTCCTCTGGGTGACCTTATTGTCTGTAATTGAAACCCTATTGAGAGGTGATGTCTGTGTTAGCCAATGACCCAGGTGAGC NM_000125.4 Homo ...
[2] TTTGATTTCCTCTGGGTGACCTTATTGTCTGTAATTGAAACCCTATTGAGAGGTGATGTCTGTGTTAGCCAATGACCCAGGTGAGC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TTTGATTTCCTCTGGGTGACCTTATTGTCTGTAATTGAAACCCTATTGAGAGGTGATGTCTGTGTTAGCCAATGACCCAGGTGAGC Consensus 

    aln (5419..5504)                                                                       names
[1] TGCTCGGGCTTCTCTTGGTATGTCTTGTTTGGAAAAGTGGATTTCATTCATTTCTGATTGTCCAGTTAAGTGATCACCAAAGGACT NM_000125.4 Homo ...
[2] TGCTCGGGCTTCTCTTGGTATGTCTTGTTTGGAAAAGGGGATTTCATTAATTTCTGATTGTCCAGTTAAGTGATCACCAAAGGACT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TGCTCGGGCTTCTCTTGGTATGTCTTGTTTGGAAAAG?GGATTTCATT?ATTTCTGATTGTCCAGTTAAGTGATCACCAAAGGACT Consensus 

    aln (5505..5590)                                                                       names
[1] GAGAATCTGGGAGGGCAAAAAAAAAAAAAAAGTTTTTATGTGCACTTAAATTTGGGGACAATTTTATGTATCTGTGTTAAGGATAT NM_000125.4 Homo ...
[2] GAGAATCTGGGAGGGCAAAAAAAAAAAAAAG-TTTTTATGTGCACTTAAATTTGGGGACAATTTTATGTATCTGTGTTAAGGATAT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con GAGAATCTGGGAGGGCAAAAAAAAAAAAAA?-TTTTTATGTGCACTTAAATTTGGGGACAATTTTATGTATCTGTGTTAAGGATAT Consensus 

    aln (5591..5676)                                                                       names
[1] GTTTAAGAACATAATTCTTTTGTTGCTGTTTGTTTAAGAAGCACCTTAGTTTGTTTAAGAAGCACCTTATATAGTATAATATATAT NM_000125.4 Homo ...
[2] GTTTAAGAACATAATTCTTTTGTTGCTGTTTGTTTAAGAAGCACCTTAGTTTGTTTAAGAAGCACCTTATATAGTATAATATATAT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con GTTTAAGAACATAATTCTTTTGTTGCTGTTTGTTTAAGAAGCACCTTAGTTTGTTTAAGAAGCACCTTATATAGTATAATATATAT Consensus 

    aln (5677..5762)                                                                       names
[1] TTTTTTGAAATTACATTGCTTGTTTATCAGACAATTGAATGTAGTAATTCTGTTCTGGATTTAATTTGACTGGGTTAACATGCAAA NM_000125.4 Homo ...
[2] TTTTTTGAAATTACATTGCTTGTTTATCAGACAATTGAATGTAGTAATTCTGTTCTGGATTTAATTTGACTGGGTTAACATGCAAA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TTTTTTGAAATTACATTGCTTGTTTATCAGACAATTGAATGTAGTAATTCTGTTCTGGATTTAATTTGACTGGGTTAACATGCAAA Consensus 

    aln (5763..5848)                                                                       names
[1] AACCAAGGAAAAATATTTAGTTTTTTTTTTTTTTTTTGTATACTTTTCAAGCTACCTTGTCATGTATACAGTCATTTATGCCTAAA NM_000125.4 Homo ...
[2] AACCAAGGAAAAATATTTAG-TTTTTTTTTTTTTTTTGTATACTTTTCAAGCTACCTTGTCATGTATACAGTCATTTATGCCTAAA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AACCAAGGAAAAATATTTAG-TTTTTTTTTTTTTTTTGTATACTTTTCAAGCTACCTTGTCATGTATACAGTCATTTATGCCTAAA Consensus 

    aln (5849..5934)                                                                       names
[1] GCCTGGTGATTATTCATTTAAATGAAGATCACATTTCATATCAACTTTTGTATCCACAGTAGACAAAATAGCACTAATCCAGATGC NM_000125.4 Homo ...
[2] GCCTGGTGATTATTCATTTAAATGAAGATCACATTTCATATCAACTTTTGTATCCACAGTAGACAAAATAGCACTAATCCAGATGC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con GCCTGGTGATTATTCATTTAAATGAAGATCACATTTCATATCAACTTTTGTATCCACAGTAGACAAAATAGCACTAATCCAGATGC Consensus 

    aln (5935..6020)                                                                       names
[1] CTATTGTTGGATACTGAATGACAGACAATCTTATGTAGCAAAGATTATGCCTGAAAAGGAAAATTATTCAGGGCAGCTAATTTTGC NM_000125.4 Homo ...
[2] CTATTGTTGGATATTGAATGACAGACAATCTTATGTAGCAAAGATTATGCCTGAAAAGGAAAATTATTCAGGGCAGCTAATTTTGC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CTATTGTTGGATA?TGAATGACAGACAATCTTATGTAGCAAAGATTATGCCTGAAAAGGAAAATTATTCAGGGCAGCTAATTTTGC Consensus 

    aln (6021..6106)                                                                       names
[1] TTTTACCAAAATATCAGTAGTAATATTTTTGGACAGTAGCTAATGGGTCAGTGGGTTCTTTTTAATGTTTATACTTAGATTTTCTT NM_000125.4 Homo ...
[2] TTTTACCAAAATATCAGTAGTAATATTTTTGGACAGTAGCTAATGGGTCAGTGGGTTCTTTTTAATGTTTATACTTAGATTTTCTT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TTTTACCAAAATATCAGTAGTAATATTTTTGGACAGTAGCTAATGGGTCAGTGGGTTCTTTTTAATGTTTATACTTAGATTTTCTT Consensus 

    aln (6107..6192)                                                                       names
[1] TTAAAAAAATTAAAATAAAACAAAAAAAAATTTCTAGGACTAGACGATGTAATACCAGCTAAAGCCAAACAATTATACAGTGGAAG NM_000125.4 Homo ...
[2] TTAAAAAAATTAAAATAAAACAAAAAAAAATTTCTAGGACTAGACGATGTAATACCAGCTAAAGCCAAACAATTATACAGTGGAAG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TTAAAAAAATTAAAATAAAACAAAAAAAAATTTCTAGGACTAGACGATGTAATACCAGCTAAAGCCAAACAATTATACAGTGGAAG Consensus 

    aln (6193..6278)                                                                       names
[1] GTTTTACATTATTCATCCAATGTGTTTCTATTCATGTTAAGATACTACTACATTTGAAGTGGGCAGAGAACATCAGATGATTGAAA NM_000125.4 Homo ...
[2] GTTTTACATTATTCATCCAATGTGTTTGTATTCATGTTAAGATACTACTACATTTGAAGTGGGCAGAGAACATCAGATGATTGAAA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con GTTTTACATTATTCATCCAATGTGTTT?TATTCATGTTAAGATACTACTACATTTGAAGTGGGCAGAGAACATCAGATGATTGAAA Consensus 

    aln (6279..6364)                                                                       names
[1] TGTTCGCCCAGGGGTCTCCAGCAACTTTGGAAATCTCTTTGTATTTTTACTTGAAGTGCCACTAATGGACAGCAGATATTTTCTGG NM_000125.4 Homo ...
[2] TGTTCGCCCAGGGGTCTCCAGCAACTTTGGAAATCTCTTTGTATTTTTACTTGAAGTGCCACTAATGGACAGCAGATATTTTCTGG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TGTTCGCCCAGGGGTCTCCAGCAACTTTGGAAATCTCTTTGTATTTTTACTTGAAGTGCCACTAATGGACAGCAGATATTTTCTGG Consensus 

    aln (6365..6450)                                                                       names
[1] CTGATGTTGGTATTGGGTGTAGGAACATGATTTAAAAAAAAACTCTTGCCTCTGCTTTCCCCCACTCTGAGGCAAGTTAAAATGTA NM_000125.4 Homo ...
[2] CTGATGTTGGTATTGGGTGTAGGAACATGATT-AAAAAAAAACTCTTGCCTCTGCTTTCCCCCACTCTGAGGCAAGTTAAAATTTA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CTGATGTTGGTATTGGGTGTAGGAACATGATT-AAAAAAAAACTCTTGCCTCTGCTTTCCCCCACTCTGAGGCAAGTTAAAAT?TA Consensus 

    aln (6451..6536)                                                                       names
[1] AAAGATGTGATTTATCTGGGGGGCTCAGGTATGGTGGGGAAGTGGATTCAGGAATCTGGGGAATGGCAAATATATTAAGAAGAGTA NM_000125.4 Homo ...
[2] AAAGATGTGATTTATCTGGGGGGCTCAGGTATGGTGGGGAAATGGATTCAGGAATCTGGGGAATGGCAAATATATTAAGAAGAGTA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AAAGATGTGATTTATCTGGGGGGCTCAGGTATGGTGGGGAA?TGGATTCAGGAATCTGGGGAATGGCAAATATATTAAGAAGAGTA Consensus 

    aln (6537..6622)                                                                       names
[1] TTGAAAGTATTTGGAGGAAAATGGTTAATTCTGGGTGTGCACCAGGGTTCAGTAGAGTCCACTTCTGCCCTGGAGACCACAAATCA NM_000125.4 Homo ...
[2] TTGAAAGTATTTGGAGGAAAATGGTTAATTCTGGGTGTGCACCAGGGTTCAGTAGAGTCCACTTCTGCCCTGGAGACCACAAATCA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TTGAAAGTATTTGGAGGAAAATGGTTAATTCTGGGTGTGCACCAGGGTTCAGTAGAGTCCACTTCTGCCCTGGAGACCACAAATCA Consensus 

    aln (6623..6708)                                                                       names
[1] ACTAGCTCCATTTACAGCCATTTCTAAAATGGCAGCTTCAGTTCTAGAGAAGAAAGAACAACATCAGCAGTAAAGTCCATG--GAA NM_000125.4 Homo ...
[2] ACTAGCTGCATTTACAGCCATTTCTAAAATGGCAGCTTCAGTTCTAGAGAAGAAAGAACAACATCAGCAGTAAAGTCCATGGAGAA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con ACTAGCT?CATTTACAGCCATTTCTAAAATGGCAGCTTCAGTTCTAGAGAAGAAAGAACAACATCAGCAGTAAAGTCCATG--GAA Consensus 

    aln (6709..6794)                                                                       names
[1] TAGCTAGTGGTCTGTGTTTCTTTTCGCCATTGCCTAGCTTGCCGTAATGATTCTATAATGCCATCATGCAGCAATTATGAGAGGCT NM_000125.4 Homo ...
[2] TAGCTAGTGGTCTGTATTTCTTTTCGCCATTGCCTAGCTTGCCGTAATGATTCTGTAATGCCATCATGCAGCAATTATGAGAGGCT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TAGCTAGTGGTCTGT?TTTCTTTTCGCCATTGCCTAGCTTGCCGTAATGATTCT?TAATGCCATCATGCAGCAATTATGAGAGGCT Consensus 

    aln (6795..6880)                                                                       names
[1] AGGTCATCCAAAGAGAAGACCCTATCAATGTAGGTTGCAAAATCTAACCCCTAAGGAAGTGCAGTCTTTGATTTGATTTCCCTAGT NM_000125.4 Homo ...
[2] AGGTCATCCAAAGAGAAGACCCTATCAATGTAGGTTGCAAAATCTAACCCCTAAGGAAGTGCAGTCTTTGATTTGATTTCCCTAGT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AGGTCATCCAAAGAGAAGACCCTATCAATGTAGGTTGCAAAATCTAACCCCTAAGGAAGTGCAGTCTTTGATTTGATTTCCCTAGT Consensus 

    aln (6881..6966)                                                                       names
[1] AACCTTGCAGATATGTTTAACCAAGCCATAGCCCATGCCTTTTGAGGGCTGAACAAATAAGGGACTTACTGATAATTTACTTTTGA NM_000125.4 Homo ...
[2] AACCTTGCAGATATGTTTAACCACGCCATAGCCCATGCCTTTTGAGGGCTGAACAAATAAGGGACTTACTGATAATTTACTTTTGA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AACCTTGCAGATATGTTTAACCA?GCCATAGCCCATGCCTTTTGAGGGCTGAACAAATAAGGGACTTACTGATAATTTACTTTTGA Consensus 

    aln (6967..7052)                                                                       names
[1] TCACATTAAGGTGTTCTCACCTTGAAATCTTATACACTGAAATGGCCATTGATTTAGGCCACTGGCTTAGAGTACTCCTTCCCCTG NM_000125.4 Homo ...
[2] TCACATTAAGGTGTTCTCACCTTGAAATCTTATACACTGAAATGGCCATTGATTTAGGCCATTGGCTTAGAGTACTCCTTCCCCTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TCACATTAAGGTGTTCTCACCTTGAAATCTTATACACTGAAATGGCCATTGATTTAGGCCA?TGGCTTAGAGTACTCCTTCCCCTG Consensus 

    aln (7053..7138)                                                                       names
[1] CATGACACTGATTACAAATACTTTCCTATTCATACTTTCCAATTATGAGATGGACTGTGGGTACTGGGAGTGATCACTAACACCAT NM_000125.4 Homo ...
[2] CATGACACTGATTACAAATCCTTTCCTATTCATACTTTCCAATTATGAGATGGACTGTGGGTACTGGGAATGATCACTAACACCAT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CATGACACTGATTACAAAT?CTTTCCTATTCATACTTTCCAATTATGAGATGGACTGTGGGTACTGGGA?TGATCACTAACACCAT Consensus 

    aln (7139..7224)                                                                       names
[1] AGTAATGTCTAATATTCACAGGCAGATCTGCTTGGGGAAGCTAGTTATGTGAAAGGCAAATAGAGTCATACAGTAGCTCAAAAGGC NM_000125.4 Homo ...
[2] AGTAATGTCTAATATTCACAGGCAGATCTGCTTGGGGAAGCTAGTTATGTGAAAGGCAAATAGAGTCATACAGTAGCTCAAAAGGC XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AGTAATGTCTAATATTCACAGGCAGATCTGCTTGGGGAAGCTAGTTATGTGAAAGGCAAATAGAGTCATACAGTAGCTCAAAAGGC Consensus 

    aln (7225..7310)                                                                       names
[1] AACCATAATTCTCTTTGGTGCAGGTCTTGGGAGCGTGATCTAGATTACACTGCACCATTCCCAAGTTAATCCCCTGAAAACTTACT NM_000125.4 Homo ...
[2] AACCATAATTCTCTTCGGTGCAGGTCTTGGGAGCGTGATCTAGATTACACTGCACCATTCCCAAGTTAATCCCCTGAAAACTTACT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AACCATAATTCTCTT?GGTGCAGGTCTTGGGAGCGTGATCTAGATTACACTGCACCATTCCCAAGTTAATCCCCTGAAAACTTACT Consensus 

    aln (7311..7396)                                                                       names
[1] CTCAACTGGAGCAAATGAACTTTGGTCCCAAATATCCATCTTTTCAGTAGCGTTAATTATGCTCTGTTTCCAACTGCATTTCCTTT NM_000125.4 Homo ...
[2] CTCAACTGGAGCAAATGAACTTTGGTCCCAAATATCCATCTTTTCAGTAGCGTTAATTATGCTCTGTTTCCAACTGCATTTCCTTT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CTCAACTGGAGCAAATGAACTTTGGTCCCAAATATCCATCTTTTCAGTAGCGTTAATTATGCTCTGTTTCCAACTGCATTTCCTTT Consensus 

    aln (7397..7482)                                                                       names
[1] CCAATTGAATTAAAGTGTGGCCTCGTTTTTAGTCATTTAAAATTGTTTTCTAAGTAATTGCTGCCTCTATTATGGCACTTCAATTT NM_000125.4 Homo ...
[2] CCAATTGAATTAAAGTGTGGCCTCGTTTTTAGTCATTTAAAATTGTTTTCTAAGTAATTGCTGCCTCTATTATGGCACTTCAATTT XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CCAATTGAATTAAAGTGTGGCCTCGTTTTTAGTCATTTAAAATTGTTTTCTAAGTAATTGCTGCCTCTATTATGGCACTTCAATTT Consensus 

    aln (7483..7568)                                                                       names
[1] TGCACTGTCTTTTGAGATTCAAGAAAAATTTCTATTCTTTTTTTTGCATCCAATTGTGCCTGAACTTTTAAAATATGTAAATGCTG NM_000125.4 Homo ...
[2] TGCACTGTCTTTTGAGATTCAAGAAAAATTTCTATTCTTTTTTTTGCATCCAATTGTGCCTGAACTTTTAAAATATGTAAATGCTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TGCACTGTCTTTTGAGATTCAAGAAAAATTTCTATTCTTTTTTTTGCATCCAATTGTGCCTGAACTTTTAAAATATGTAAATGCTG Consensus 

    aln (7569..7654)                                                                       names
[1] CCATGTTCCAAACCCATCGTCAGTGTGTGTGTTTAGAGCTGTGCACCCTAGAAACAACATATTGTCCCATGAGCAGGTGCCTGAGA NM_000125.4 Homo ...
[2] CCATGTTCCAAACCCATCGTCAGTGTGTGTGTTTAGAGCTGTGCACCCTAGAAACAACATATTGTCCCATGAGCAGGTGCCTGAGA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CCATGTTCCAAACCCATCGTCAGTGTGTGTGTTTAGAGCTGTGCACCCTAGAAACAACATATTGTCCCATGAGCAGGTGCCTGAGA Consensus 

    aln (7655..7740)                                                                       names
[1] CACAGACCCCTTTGCATTCACAGAGAGGTCATTGGTTATAGAGACTTGAATTAATAAGTGACATTATGCCAGTTTCTGTTCTCTCA NM_000125.4 Homo ...
[2] CACAGACCCCTTTGCATTCACAGAGAGGTCATTGGTTATAGAGACTTGAATTAATAAGTGACATTATGCCAGTTTCTGTTCTCTCA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CACAGACCCCTTTGCATTCACAGAGAGGTCATTGGTTATAGAGACTTGAATTAATAAGTGACATTATGCCAGTTTCTGTTCTCTCA Consensus 

    aln (7741..7826)                                                                       names
[1] CAGGTGATAAACAATGCTTTTTGTGCACTACATACTCTTCAGTGTAGAGCTCTTGTTTTATGGGAAAAGGCTCAAATGCCAAATTG NM_000125.4 Homo ...
[2] CAGGTGATAAACAATGCTTTTTGTGCACTACATACTCTTCAGTGTAGAGCTCTTGTTTTATGGGAAAAGGCTCAAATGCCAAATCG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con CAGGTGATAAACAATGCTTTTTGTGCACTACATACTCTTCAGTGTAGAGCTCTTGTTTTATGGGAAAAGGCTCAAATGCCAAAT?G Consensus 

    aln (7827..7912)                                                                       names
[1] TGTTTGATGGATTAATATGCCCTTTTGCCGATGCATACTATTACTGATGTGACTCGGTTTTGTCGCAGCTTTGCTTTGTTTAATGA NM_000125.4 Homo ...
[2] TGTTTGATGGATTAATATGCCCTTTTGCCGATGCATACTATTACTGATGTGACTCGGTTTTGTCGCAGCTTTGCTTTGTTTAATGA XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con TGTTTGATGGATTAATATGCCCTTTTGCCGATGCATACTATTACTGATGTGACTCGGTTTTGTCGCAGCTTTGCTTTGTTTAATGA Consensus 

    aln (7913..7998)                                                                       names
[1] AACACACTTGTAAACCTCTTTTGCACTTTGAAAAAGAATCCAGCGGGATGCTCGAGCACCTGTAAACAATTTTCTCAACCTATTTG NM_000125.4 Homo ...
[2] AACACACTTGTAAACCTCTTTTGCACTTTGAAAAAGAATCCAGCGGGATGCTCGAGCACCTGTAAACAATTTTCTCAACCTATTTG XM_009452243.3 PR...
[3] -------------------------------------------------------------------------------------- XM_015137107.2 PR...
Con AACACACTTGTAAACCTCTTTTGCACTTTGAAAAAGAATCCAGCGGGATGCTCGAGCACCTGTAAACAATTTTCTCAACCTATTTG Consensus 

    aln (7999..8024)           names
[1] ATGTTCAAATAAAGAATTAAACTAAA NM_000125.4 Homo ...
[2] ATGTTCAAATAAAGAATTAAACTAAA XM_009452243.3 PR...
[3] -------------------------- XM_015137107.2 PR...
Con ATGTTCAAATAAAGAATTAAACTAAA Consensus 

Pathway Analysis Since Pathway analysis directly connects to the results of RNA-seq, once the previous coding error unde the RNA-seq data is worked out, pathway analysis will be shown, for now, below is a comment of the skeleton of the input

#go<- goana(tr, species= "Homo Sapien") 
#topGO(go, n=15)
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